Yes, Jamie answered the situation as he did me when I had the problem, the easiest way to get around this is to go 4 analog in's into the 744 to stay away from the "latency" issue, or get your v3 serviced by grace.
To fix the problem, Just invert the phase for the 2 channels that went digi into the 744, before combining all 4 files...
Its not always that noticable, but once you know of the problem, and start listening, it will stand out like a sore thumb.
Have you guys tried 2 digi in's into the 744 yet?