Admittedly I haven't had an opportunity to play the actual Amiga version of Lemmings. However, comparing that mod to various other versions of the tune with the similar arrangements (Windows, Dos, PS1... even the Classic music from Lemmings 2) it becomes clear that the Amiga mod version differs... In an early part of the tune, on a rhythm where the other versions have percussion, the Amiga mod uses a non-percussive sample. Same beat, same timing... vastly different sound.
Taking a closer look, while the only percussive sample included is in the second slot, the note patterns appear to be also trying to use the fifth sample in a percussive manner.