Hum.. I’m still convinced it is the 44.1K vs 48K causing your problem. The 44.1K frequency is perhaps being sped up ever so slightly to increase its frequency to 48K causing it to shorten ever so slightly over time.
Try changing your timeline in FCP to 44.1K. Click somewhere in your timeline (anywhere, so the timeline box is active.) From the sequence drop down choose ‘Settings’, and choose 44.1K. Now delete the audio track from the sequence, then replace it, so it’s freshly inserted into the timeline.
Colin McQuillan
Van. B.C.