Are you triggering the cameras, or simply acquiring from a fixed sampling rate.
The difference could be that both cameras are not running at 100% the same frequency. If one delivers pictures at 1Hz, and the other one at 1.05Hz, then after several captures, you'll notice a difference.
If you're triggering the cameras, then this shouldn't be the problem as your program is synchronising the two cameras.
I've had this "problem" with multiple parallel serial instruments. I ended switching to a queue-based producer-consumer model, and everything worked great.
Hope this helps.
Shane.
Using LV 6.1 and 8.2.1 on W2k (SP4) and WXP (SP2)