They are NOT wholly hadware config related issues and are quite easy to replicate.

I can't vouch for the Matrix since I really don't use it, but I'd be interested in seeing a reliable, hardware-independent recipe for reproducing a VSTi sync issue not involving the Matrix. The one you used to report this bug to the Bakers should do nicely. 

brundlefly

One bonafide bug to be aware of is that having a MIDI FX on any track (regardless of which one, and whether enabled or not) will cause SONAR to play some notes from the measure following the end of the loop range.

AHA, so It's a MIDI FX on the track that causes this?

It's been driving me NUTS, I can live with the out of sync issue, but having to move every clip away from the range that's looping so this "bar from next clip playing at loop turnover" is impossible to ignore, so I end up having to move every clip a bar away from the loop, then move everything back when done.

Only problem now is that I use a few different keyboards when playing parts that need keyswitches (88 key one for playing and a 49 key for the keyswitches) and I use the transpose plugin to move the range so they can be played on the 49 keys so I don't have to transpose the keyboards all the time.

Hmm, time to break out BOME midi translator again 

I found a timing problem a while back when trying to sync to SMPTE.  Yeah I know...who in the world sync's to SMPTE these days?  Well...I did up until Sonar X1.

What I found is...that everything will play back in sync to SMPTE EXCEPT soft synths.  The same thing happens as what was described above....the longer it plays the further out of sync it becomes.  Stop and restart playback and everything is in sync again....for a time, then starts drifting off again.

Audio tracks and midi hardware tracks will stay in sync with SMPTE for ever.....but NOT soft synths.  Strange, but true... :) .