rogeriodec

Base 57
The short answer is the "Timing Offset" in the "Sync and Caching" page of "Preferences" can be adjusted to offset midi recording in the manner you are looking for.

Here is the answer! 
Thank you Base 57!

My understanding is that this setting deals only with audio not midi. So I believe that this is not the correct answer. It seems there is no answer to prevent this from happening. It has to be corrected after the fact.

pinguinotuerto
My understanding is that this setting deals only with audio not midi. So I believe that this is not the correct answer. It seems there is no answer to prevent this from happening. It has to be corrected after the fact.

It worked for me. See the help: http://www.cakewalk.com/Documentation?product=SONAR&language=3&help=0x22B1A
 
Timing Offset (msec). With this option, used for making very fine adjustments to the audio/MIDI synchronization of your project, you can offset the audio in your project by a number of milliseconds. A positive value delays audio by that amount. A negative value delays MIDI by that amount.
 

rogeriodec

pinguinotuerto
My understanding is that this setting deals only with audio not midi. So I believe that this is not the correct answer. It seems there is no answer to prevent this from happening. It has to be corrected after the fact.

It worked for me. See the help: http://www.cakewalk.com/Documentation?product=SONAR&language=3&help=0x22B1A
 Timing Offset (msec). With this option, used for making very fine adjustments to the audio/MIDI synchronization of your project, you can offset the audio in your project by a number of milliseconds. A positive value delays audio by that amount. A negative value delays MIDI by that amount.
 

I thought this setting was for when Sonar is being used as a slave chasing time code from another source. I will mess with it and report back. If this solves the problem, then you've solved an issue nagging many of us for a long time.

Didn't do anything for me.

Timing Offset may look like it's only applicable to the Chase Lock setting, but it's active regardless of whether Trigger and Freewheel or Chase Lock is selected. Its original intent was to allow syncing audio to MIDI-driven hardware synths on playback. But since it works by shifting the M:B:T grid against the audio clock, it will alter where MIDI lands on the grid when recording to the audio metronome.
 
If you only ever use soft synths, it might makes sense to solve a MIDI record timing problem with this setting because soft synths are handled like audio. But if you use hardware synths, having a large positive offset to make MIDI land later on the grid while recording will conversely cause it to be sent early vs. audio on playback. The bigger the offset, the more it will work against you on playback. But, again, this will only be a problem if you use hardware synths.

brundlefly
Timing Offset may look like it's only applicable to the Chase Lock setting, but it's active regardless of whether Trigger and Freewheel or Chase Lock is selected. Its original intent was to allow syncing audio to MIDI-driven hardware synths on playback. But since it works by shifting the M:B:T grid against the audio clock, it will alter where MIDI lands on the grid when recording to the audio metronome.
 
If you only ever use soft synths, it might makes sense to solve a MIDI record timing problem with this setting because soft synths are handled like audio. But if you use hardware synths, having a large positive offset to make MIDI land later on the grid while recording will conversely cause it to be sent early vs. audio on playback. The bigger the offset, the more it will work against you on playback. But, again, this will only be a problem if you use hardware synths.

Then I need to experiment with it more to see if I can resolve this issue. I'll try again and post my results. Thanks for clarifying that. Perhaps Cakewalk should separate or differentiate that setting visually from the Chase and Lock setting so that users can be aware that it isn't only active when Sonar is in slave mode.

Yes, the preferences layout has had Timing Offset indented like that forever - not sure why. Just one of those endearing little quirks of which SONAR has so many. 
 
Personally, I prefer to just run audio latency as low as possible, get audio record latency compensation dialed in, and ignore MIDI latencies that are typically an order of magnitude lower than my sloppy expressive performances. Timing Offset introduces more potential complications than its worth if you're correcting more than a few milliseconds. And on my system, MIDI record timing is (and has always been) just as expected - a few milliseconds later than perfectly-compensated audio due to uncompensated MIDI transmission latency.

So, it solves the problem, but not if you follow Cakewalk's instructions on what this setting does (unless I'm understanding it backwards). The documentation says, " A positive value delays audio by that amount. A negative value delays MIDI by that amount."
If I enter a negative value to delay MIDI, my MIDI lands even earlier in relation to the Audio. Conversely, if I enter a positive value (which I noticed rogeriodec did- probably unwittingly) my MIDI does line up with my audio and the metronome.
The value I entered was the exact same value I was entering before into my nudge settings, but I converted it into milliseconds, instead of using samples. So the value has to be whatever your Roundtrip Audio Reported Latency is. which appears in the same preferences window (Synch and Caching) all the way at the bottom. To convert from samples to milliseconds, take whatever sampling rate you're using (44.1 or 48) divide it by 1,000 (result will be 44.1 or 48) and then divide your Audio Reported Latency by that number (44.1 or 48) to get the milliseconds you need. This will all line up and work as long as you have the Use Audio Reported Latency box checked.
 
 

The documentation is correct. A positive value delays audio (including the audio metronome) relative to the MBT grid. That means you'll hear the metronome click after the Now time crosses the grid beat, causing you to play late relative the grid so your MIDI lands later than it otherwise would.

brundlefly
The documentation is correct. A positive value delays audio (including the audio metronome) relative to the MBT grid. That means you'll hear the metronome click after the Now time crosses the grid beat, causing you to play late relative the grid so your MIDI lands later than it otherwise would.

I'm still a little confused. If that were the case, wouldn't the pre-existing audio tracks be delayed also causing them to fall behind the newly delayed MIDI anyway, therefore leaving everything out of synch still?
What seems to be happening is that the MIDI is now landing where the audio was landing originally and they are in synch. The original audio was recorded to the metronome before the change was made to the settings, so if the metronome were now playing later than it did before, things wouldn't line up like they are. The metronome seems to be playing just like it did before, but the MIDI lands now where it is supposed to in relation to the audio.  My head is spinning. Although I'm glad the problem is solved.