I have two instances of AD2.  One instance is just some percussion pieces on MIDI channel 10 and the other instance is a drum kit (Fairfax) on MIDI channel 9.  Using the step sequencer I created an 8 beat, 4 step pattern for both the project is at 108 beats per minute.
By the time I get 15 or 20 measures into the tune the 2 instances of AD2 are starting to get out of sync.
Any ideas?
If this is the wrong place to post this can someone point me in the right direction.
 
TIA
rafone

What happens if you enable the metronome , just for kicks, to see if the AD timing is affected?
 
I remember there were some midi timing issues with looping that could be affected positively by turning on SONAR's built-in metronome click.

The timing issue that was solved by turning on the metronome and muting it was more to do with a drift which appeared after multiple iterations of a loop, and it was fixed I believe. I certainly haven't seen it for a while. 

Enabling the Metronome may still help identify where the problem lies if one of the tracks remains in sync with it and the other doesn't. I'm not able to reproduce a problem, but if it's a bug I would guess it's something to do with Step Sequencer. You might try bouncing the clips to regular MIDI.
 
Incidentally, it's not necessary to use separate MIDI channels as each instance of the synth effectively has its own MIDI port.

Enabling the Metronome has confirmed that the two are not in sync.  I am using the step sequencer.  Both instance have a 2 measure sequence with just straight ahead 8th notes.??
Only one is out of sync. 

So, can you tell if they are both drifting or is it just one?
 
The answer will help you decided what to do next