I have to agree with the comments about not connecting and disconnecting things while Sonar is running.  It even states somewhere in the documentation to hook up midi controllers, interfaces, etc. before opening Sonar. 
 
I have had very few problems with X3d, even with my fairly minimal system.

This is worth the read.
 
http://www.harmonycentral.com/t5/Technology-Computers/Solving-the-Windows-MIDI-Port-Problem/ba-p/34667124
 

sycle1
I have it on good authority a majority of HDD don't last more than 2 years at the best of outcomes and Power supplies get flakey all the time but I ain't an IT guy!

That may have been true 5 years ago (although I would have said three years), things have got a lot better nowadays. Every now and then there are a faulty batch of hard drives which kills this opinion.

sycle1
I have it on good authority a majority of HDD don't last more than 2 years at the best of outcomes and Power supplies get flakey all the time but I ain't an IT guy!
But you can blame SONAR for this if ya want too!
But it Doesn't seem to worry me
How old is your Hardware?????
 

 Your so called "good authority" is clueless.   I still have IDE drives from the last century that still work. Quality power supplies don't get flakey all the time.  You aint a hardware guy either.
  If the problem was a drive or RAM it would exist in Windows as well.
 

henry1491
As a (very very very) long time cakewalk user I've become accustomed to (every once in a while) a release being, uhmm, 'a bit of a chore to use', and yet, with the X-series, I've begun to 'believe' again... at least until X3(d) (Producer)...
 
Simply, it routinely keeps freezing.  Hanging for 30-60 seconds, to the extent that Windoze 8 (64) routinely notes it as 'not responding'.  This on the same rig, same everything in fact, that ran X2 'perfectly'.  This is clearly utterly unacceptable.  To the extent I'm genuinely and seriously considering regressing to X2.
 
It also cannot reliably remember MIDI ports, so I routinely get asked if 'MIDI Port A' is the same MIDI port as 'MIDI Port A'.  Particularly if I've turned on (or off) a device that has a USB MIDI connection before/after a software restart.  This suggests a problem in X3's underlying configuration/control/mapping files when working with a USB MIDISPORT 4x4 and (directly) USB MIDI connected devices.
 
I also note that when connecting a device (esp a direct USB linked device), despite it having been previously configured, I have to go back in to the MIDI configuration to re-enable the MIDI device and further, re-assign its MIDI instruments.  This further suggests a problem (aka sporadic corruption) in X3's underlying configuration/control/mapping files.
 
X3d has also completely forgotten/lost (initially mid session, but continuing after a total PC power-down & reboot) my connection to my Frontier Alphatrack.  This happened after I (USB) detached and reattached my Korg Nano Key2.  This has NEVER happened before.  Ever.  This confirms a problem (aka sporadic corruption) in X3's underlying configuration/control/mapping files - even when not changed by the user.
 
As an experienced IT developer (working in real-time zero-loss messaging systems) this is irritating.
 
X3d is also routinely immune to mouse/keyboard/all other inputs, or indeed any form of input - to the extent that I thought my keyboard/mouse/Alaphatrack had become faulty.  I assume this to be a minor variant of the whole 'application simply freezing' (as noted above).
 
Additionally, if I save 'project v1.2' as 'project v1.3' in X3, and then close X3 by shutting down Windoze (e.g. not shutting the application itself directly), the next time I start X3 it has no memory of '...v1.3' in its startup menu.  Yes I accept this is trivial, but it is still poor, and a further exemplar.
 
So for 70% of the time X3d works faultlessly....... but that's down from 95% with X2... and about 20% less than I'd expect from any software... even freeware.
 
Honestly I do genuinely hate to moan, and I really do appreciate that trying to develop software for a near infinite number of PC variants must be a bloody nightmare, but I'm really not happy at the moment.
 
So, in summary, if you want someone to beta test X3e (or X4), please do get in touch.  I'm happy to sign an NDA.
 
All of that said, thanks for sorting out the atrocious 'magnetic' drag and drop MIDI note (non)alignment debacle... albeit that should never have passed testing... and on the plus side, your email and phone support is actually pretty good + very friendly.

  I'm not sure everyone understands what you are doing.  If you are having these problems in Sonar, demo another DAW and see if it's happening too.  That would at least point a direction.  I can't see this being a Sonar problem. BTW please don't be intimidated by the fanboys here by adding an apology in your title.
 
 Any reason you are still using a MIDISPORT 4x4?  I'm not a fan of M-Audio drivers.  Odd as it is I still have a 1st generation Oxygen 8 that would not be recognized in the Sonar X series.