Well, there is nothing that can be really done here apart from disabling on-the-fly sample swapping, because the module is showing clear signs that sample swapping should be used while in reality it should not. ProTracker is not the only tracker supporting sample swapping so I would be reluctant to unset this flag just because the module wasn't made on Amiga (since it has out-of-range notes). This is why the flag can be toggled by the user, after all.
The only "real" bug here is that having ProTracker one-shot loops enabled also causes this behaviour, and one-shot loops really should be disabled for modules that were not made on Amiga.

r6357 fixes that one-shot loops are not enabled anymore for this module, but the sample swapping will have to stay enabled, I'm afraid. As said, this is why you can manually disable it.