Morvejones:
This sound a lot like a problem that I had under Sonar Producer X3.
I was doing loop recording with the metronome on with count in. It would seem to record fine, but when I stopped each take was incrementally offset by the count in. Because the beginning of each take was incrementally increased by the count in, each take would "wrap around" into the next by an amount equal to the incremental offset causing each take to be more and more out of sync.
Is that what you are seeing?
Paul