I created a midi clip consisting of short notes to be played through the GSi VB3 softsynth. Although the notes are quantised, the timing sounded off, so I tried bouncing to audio to see what is going on. Sure enough, the audio waveform shows that most, but not all, of the notes are playing early, by as much as 25ms.
 
I directed the midi to a different softsynth (Rapture) and bounced to a new audio track. This time the timing all looked (and sounded) correct. I guess that the problem must be with VB3, unless anyone has any other suggestions.
 
[Sonar X2a, 32-bit (project originally created in Sonar 7 on different platform).
No effects used.]

This has been reported before with a possible solution here http://forum.cakewalk.com/FindPost/2731416

Thanks for the link.  I am not sure if this is the same problem though.  My midi timing is not consistently off by a fixed amount.
 

I have just tried opening the project in Sonar 7 to see if that would make any difference.  No, same behaviour.  Next I fired up the old XP platform and opened the project in Sonar 7 there.  Midi timing is perfect on my old system.  Go figure!