Try to compare the number of actual frames like 42347 vs. 42345.
I think you might be looking at QT tc vs. FCP tc.
what are the actual number of frames. You can view both files in FCP.
There is really no difference between 23.98 and 23.976 contrary to popular belief.
David.
PS; haw does loosing these two frames matter?
Please also make sure you are view NON DROP FRAME tc in both sources.