I think this is just because of the EF command being used in the song (e.g. on row 0 of pattern 3).
It's supposed to invert the sample loop during playback, but the change is actually done directly to the sample.
This causes the sample to sound different during each playthrough.
This is intended behaviour, and occurs in ProTracker (and similar trackers) too.

Maybe not intended (many people don't check whether their tracks loop cleanly), but OpenMPT's behaviour is definitely technically correct. The invert loop effect last seen in pattern 12 is never turned off, so it keeps inverting sample data for all subsequent playback.