I notice some glitches in the music here and there but this is happening on a lot of levels not just Mayhem 2.
Well, this is strange, as I played every level and only that one has that problem.
I notice that you've replaced the levels with the Amiga versions (that have all those water and other objects that are missing in the DOS version).
Of course, this is the purpose of the "corrected version" to have it to be like the Amiga version.
So my conclusion is that maybe there's your reason why they took out all those "missing" water and objects in the DOS version. Maybe the game just can't keep up when you put back in those additional objects, and the glitches in the music is one of the symptoms of the game starting to lag.
I don't know exactly how the executable is running, but I thought that when a level is loaded, it only keeps the actual level in memory and NOT the others. Tell me if I'm wrong. In Mayhem 2, there are not a lot of objects compared to some other levels and I thought it would keep the actual level objects in memory without affecting anything else.
However, I tested Mayhem 2 with lem-fix2.exe and there wasn't that problem again (it was another song). Therefore, I didn't encounter any sign of lags. But I didn't test all the levels with that version. I'm curious, if you use that version instead, does the same music glitches happen?