From this thread...
http://forum.cakewalk.com/Rapture-puzzles-m2971217.aspx
in January, B Rock says this...

b rock 
One very cool thing that you haven't mentioned in the reported Envelope Follower capability (I don't have a GR-20; just the ancient GR-1).  I'd be all over that one.  It looks like it will transmit a CC18 MIDI message value (under certain conditions) that varys according to guitar amplitude.  A versatile feature just aching to be tapped.  Say, cutoff frequency of a resonant filter?  Technique-controllable synth 'envelopes'?
 
I think if you look at page 29 of the GR-20 manual (and also the MIDI Implementation Chart towards the back), you'll find a lot of the background information that you'll need for some deeper experimentation.

 
I hunted out the old thread today and tried to figure out how to make it work.
Here is a video of me messing around with it...
http://youtu.be/zPOn76R5zd0
 
What's cool here is that the GR20 reads the decay on the strings and that decay envelope can be used to automate parameters in the Synths.
 
I think it's outrageous fun!
 
B Rock, many thanks!!

Nice "follow" through.  Your enthusiasm is infectious, and I know the feeling well.  I do something quite similar with my Lexicon MPX-1; generating envelope-controlled MIDI from the audio input, or triggering its own ADSR envelopes shaped internally.
 
I noticed that you're using direct MIDI Learn control.  There are some great advantages to that route: easy to implement, single source over multiple controls, visual feedback on the controlled parameters, reverse (as you demonstrated), 2 varieties of high & low limits on the parameter travel.  Plus, it remains locked across all presets and all synth instances until you clear the configuration file or 'MIDI Forget' it.
 
You've probably figured out that another method uses the MIDI or Modulation Matrices.  Another set of advantages there.  Parameters that are inaccessible through any other routing.  Control over the same parameter on each Element ("All" destinations).  Smoothing over input, 'reversed' or extended parameter depths, and much more.
 
z3ta+s matrix allows even more configuration options.  Curves, function 'matrix-within-a-matrix', blending with synth LFOs and envelopes, ... the list goes on.  I find envelope control from the guitar to be even more expressive than MIDI keyboard controllers with a full complement of aftertouch, wheels, knobs and such.  There's a goldmine of expressivity there with the GR-20 MIDI output.  Have a blast.

B Rock,
 
When you say "MIDI or Modulation Matrices" are you meaning like the Synth Control Bar shown in this link?
http://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=Browser.10.html
in Figure 218. Synth control bar?
 
I do know about the Mod matrix at the bottom center of the Zeta2 Synth tab (as opposed to FX tab).
P36 of the Rapture Help file.
 
This is my biggest struggle...
The foot pedals for Glide and Hold are also for changing patches depending on a button I push on the guitar.
I often use the glide and hold foot pedals.
If I accidentally step and change patches, Rapture stops working.
 
!!It's taking me forever to post this because I keep stopping and playing for hours!!
 
I know that there is the Midi Filter plugin and also the
http://www.cakewalk.com/Documentation/help.aspx?hid=0x2015F&prod=SONAR%20X3&lid=3
I went into this and select None - then checked only NOTE. I stepped on the patch change pedal and Rapture stopped working.
 
Now, if I set rapture to some unused midi input - like UCX Midi Port 2 ch 16, I can change patches on the GR20 without messing up Rapture.
 
To fix the problem with Rapture, I have to close out of Rapture and re-open without saving. If I save, I might have to drop Rapture from the project and re-Insert it.
 

I meant the Rapture or z3ta+2 matrix that's integral to the softsynth itself.  It sounds like you're aware of the z3ta+ one (although the depth of that matrix deserves it's own book).  In Rapture, it's the 3rd of four icons just to the left of the RAPTURE logo on the synth.  It looks like a MIDI jack.  From memory; I don't have the help file handy.
 
SOURCE would be CC#18 for your envelope follower control.  DESTINATION is your targeted parameter(s).  DEPTH is self-explanatory (although sometimes - like with LFOs - you'll need the modulator enabled / Status:On to affect it).  SMOOTH adds a "curve" to your input to round out the rough spots.
 
As for your main problem ... I can tell you what I do.  It may or may not help, it costs, but I never have to concern myself with it again.  I filter any errant MIDI messages before they ever reach the computer.
 
MIDI Solutions Event Processor  MIDI Solutions Event Processor Plus
 
I use strictly MIDI DIN inputs for the non-keyboard connections, and the EPP is on a MIDI router port.  No USB for the guitar stuff, so that can be problematic in some setups.  The EPP is MIDI-powered, not the easiest thing to program, but once you do, it stays set.  I've developed dozens of useful scripts with it, and these little boxes can do just about anything.  Miniature MIDI toolkits.
 
That may not be a viable option for you.  I'm sure that there are other ways to pull this off ITB.  I simply never concerned myself with them once I found a foolproof option that I could set-and-forget.
 

Hmmm. It's not way out of range. I'll have to save for it, but it should be doable.
 
https://www.youtube.com/watch?v=51o-IRKx0aY
 
I made another video and you can see in the video at the end the sound spikes and the RME cuts it off. I'm not sure what the situation was that the sound was going bad... just too loud?

I didn't get to the 2nd video yet, but I tried a quick experiment after I got back to the studio.  I'm using a MIDI keyboard controller to simulate your GR20 setup, so this may take a little bit of back-and-forth to get it right.
 

I know that there is the Midi Filter plugin and also the
http://www.cakewalk.com/Documentation/help.aspx?hid=0x2015F&prod=SONAR%20X3&lid=3
I went into this and select None - then checked only NOTE. I stepped on the patch change pedal and Rapture stopped working.

 
In a fresh project [X2 currently there], I loaded up an instance of Rapture.  The keyboard was sending MSB/LSB bank changes and program changes.  In the FX Bin of the MIDI track-half, I loaded the MIDI Event Filter (MIDI FX plugin).  Like you, I selected None (the default).  Then, I enabled Controllers (only), to allow simulated CC messages from the GR20 for the envelope follower, modulation, etc.  You may want to enable Wheel messages as well.  I don't believe that to cause any problems, and you'll want it for the GR20 feature set.  Toggle Wheel events on & off during every other test run.
 
Now, the important part:  I reduced the Controllers range from the default 0-127, down to 1-119.  Throwing all kinds of patch & bank changes at Rapture, I never experienced the "silent treatment".  I still think that it's the CC0 bank change message - transmitted with your patch changes - that's causing the problem here.  I excluded the CC messages from 120-127 for good measure (there are some reasons for that).
 
If this works for you, then we're good.  If not, report back.  We may have to also exclude CC32 bank changes, scattered RPN/NRPN parameters, and/or sysex messages as well.  I have a few more options, and another MIDI FX freebie in mind: TenCrazy's Track Doorman (untested at this point).  Good luck.

Ok, I gave it a good try.
 
https://www.youtube.com/watch?v=P3KFP1D6qgw
 
The only thing I've found that works also makes the synth make no sound. By this I mean, if I use the Midi Event Filter plugin to exclude non-special events on channels 1-6 then using the batch change button on the GR20 does not cause Rapture to stop working.
 
I wasn't able to get it so I can play the synth and use the patch change pedal.

Well, you're trying everything that I would try, including the Event List View.  I'm thinking that the problematic events are getting to Rapture prior to filtering.  That is, the renegade events are still being recorded, but filtered out by the MIDI Event Filter MFX on playback.  The damage is already done.  As I said above, my personal process is filtering by event processing before external MIDI ever reaches the DAW.
 
Have you tried disabling Patch Changes (and System Exclusive) in Edit -> Preferences -> MIDI ->Playback and Recording ->Record?  That might not do it all, but perhaps in combination with filtering CC0, etc. ???
 
You mentioned the large bank values in the video.  Here's the official (X2) explanation: Assigning The Bank Select Method.  There are a couple of threads in the Sonar & Instruments forums that I'll have to dig up involving bank change bugs.  That Normal* - 0-bank 0 situation has always given me fits, and it's problematic for z3ta+ bank changes, too.  One of the suspects worth investigating, but I don't believe it to be the root cause here.
 
I'm at a big disadvantage trying to 'simulate' a GR20 on this end.  I'm close to saying that I'm stumped here, but irritated enough to keep looking for another solution.  And if the workaround becomes too convoluted, then I'll have to give up.  But I have one more wild thought that just may do the trick ...

B Rock,
You've been a tremendous help!
 

B Rock, Master of Midi
I'm thinking that the problematic events are getting to Rapture prior to filtering.  That is, the renegade events are still being recorded, but filtered out by the MIDI Event Filter MFX on playback. 

 
You are right about this. I tested by recording with the filter on and stepping the patch change pedal. After I stopped recording and removed the filter (since it filters channels 1-6 as showing in the video) I was able to play the synth.
 
Similarly if I play over the clip without the filter on, it stops Midi from working on the Synth.
 
Here's a link to the midi causing my issue in a groove clip...
http://stabilitynetwork.blob.core.windows.net/g-tunes/MidiEventsCausingIssue.mid
 

B Rock, the great!
Have you tried disabling Patch Changes (and System Exclusive) in Edit -> Preferences -> MIDI ->Playback and Recording ->Record?  That might not do it all, but perhaps in combination with filtering CC0, etc. ???

 
I had tried this but not in conjunction with looking at the Event List. The events recorded change when you uncheck Patch Changes in Preferences > Midi > Playback and Recording. Suddenly I could see the Control 0 and Control 32 messages.
 
Next, I also unchecked Controller in Preferences > Midi Playback and Recording. This does the trick!
 
!!!!!!!!! PROBLEM SOLVED !!!!!!!!!!!!!!
 
YAY!!
 
Thanks!!
 
And Thanks to Scook too, who first pointed me to unchecking the Patch Changes. I just need to go one step further.
 
 

EDIT:  I guess that I should've refreshed the page before I worked out another solution.  Either way, I'm glad that the problem is solved.  And you don't know *how* glad.  I may have been bugging me as much as it did you.
 

But I have one more wild thought that just may do the trick ...

 
And here it is.  Yes, it is a crazy solution.  But I think this will work in your configuartion.
 
It involves the LoopBe virtual MIDI cable trick and one additional MIDI track.  Scook pointed you to the links. 
Here's the routing:
 
Track 1: VMC (additional) MIDI Track = GR20 Input -> MIDI Event Filter [MIDI FX bin] -> LoopBe MIDI Output
Track 2: Rapture MIDI Track (half pair) = LoopBe MIDI Input -> Rapture (audio) Synth Output (armed for recording)
Track 3: Rapture Audio Track (half pair) = Rapture Primary Stereo -> Master
 
It's the same Rapture pair of tracks.  You're simply inserting a virtual MIDI cable between the GR20 and the normal Rapture input routing.  And you're using an additional MIDI track to house the MIDI Event Filter MFX.
Here's the concept:
 
Track 1 will filter out the renegade events before they ever get to Track 2.  The filtered results get transferred to & recorded onto Track 2.  Rapture (on Track 3) never 'sees' the events that are causing it to go silent.
 
The same concept works for recording Draw Tool automation, live recorded arpeggiator output, MFX transposed notes, echo delay, velocity processing, and other MIDI FX options.  Note that it doesn't work with *all* MIDI FX (some add All Notes Off and other blocking messages).
 
Effectively, you're using the additional MIDI track for playback, then recording the results (including MFX processing) onto your 'normal' MIDI track.  It may be the option that works for you.  One more note:  Route one track *directly* to the next.  No Omni or None input shortcuts.  There is such a thing as a MIDI feedback loop, and that will bring everything to an immediate halt.  Good luck.