This is driving me nuts! :p
I have done some more testing.
To be clear, I am running an iPad2 with all background apps closed. The iPad has been restarted before testing.
It seems to happen more often when working with M4A/mp3...
When it comes to WAV, it is not easy to pinpoint what is causing the timing errors.
I have tested for audio length, zoom level and track count.
To reproduce the errors I see, please follow this revised procedure:
1. Create new project
2. Import WAV audio file to track 1
3. Mixdown project and select options to separate tracks and select WAV
4. Add new audio track
5. Doubletap the mixed down track to import it again
6. Zoom all the way in and check that the two tracks match exactly in time.
Now hopefully so far this should be OK, when working with WAV. But... lets increase the track count from 2 to 4:
7. Repeat steps 4 to 6, (or copy and paste track 1 to track 3 and track 2 to track 4) so that you have 4 tracks in total.
8. Mixdown project again with options to separate tracks and select WAV. This will give you 4 new mixdowns.
9. Repeat steps 4 to 6 with the new mixdowns, so you have 8 tracks in total.
10. Look at the last couple of tracks and compare timing with the original track 1.
11. Still OK?
If you import an mp3 in the first step, you will most likely see the timing issue in the first mixdown...
I have attached some screendumps of the problems I encounter using mixdown.