OpenMPT mostly goes after ProTracker 2.3, which is without doubt the most used ProTracker version. ProTracker 3 differs from that in various subtle and not-so-subtle ways since it tried "fixing" glitches from PT1/2, and I will keep sticking to the PT1/2 behaviour.

Thanks for the quick response. I tried again with ProTracker 2.3d. It sounds very similar to 3.61. It seems like 2.3d switches to the new instrument once the original one hits the end and starts looping. Oddly the "Sampler" view still thinks that the original instrument is the one playing. With the speed of the song and the samples involved the difference between the 2.3d and 3.61 behaviors is hard to hear. PT 3.61 definitely waits until the next note to switch instruments. Either of these behaviors sounds better than the "switch to the new instrument immediately" behavior though.

Yes, PT1/2 play the old sample until the loop point, which is often not noticeable. Anyway, I have changed this to use PT3's behaviour since this is more in line with some other trackers as well. The same fix has been applied to the S3M player, since ScreamTracker 3 does the same.
Here's a fixed version: http://sagagames.de/stuff/mptrack.exe

Sounds good! Thanks.