Don't rest just yet. I finally found the first real issue with your MODs.
Compare your version of Lemming2 to the one on the jukebox (
http://www.deveria.com/alexis/lemmings/lemmings/music/lemjuke.html, Track 4). You can stop listening as soon as the main melody starts.
Notice that in your version, at least when I played it on DeliTracker, you have an instrument sound that resembles a high-pitch snare drum (as opposed to the other snare drum sound, which is lower pitched and louder). But in the jukebox version, that same instrument is decidedly not a snare drum sound. If this isn't clear, the difference should be very noticeable in that measure that was immediately before the main melody, the measure leading directly to the start of the main melody.
I checked the jukebox version against both the game as played in WinUAE (admittedly with the AFS rather than your IPF), and also the Cust.Lemming rips played on DeliTracker. Those are all the same; yours is different.
Explanation please?
I should note that in pointing this out, my assumption was that your MODs are supposed to be exact replicas of what the music would sound like if I were to play the game on its original Amiga disks on the real Amiga. If instead it's the case that you are deliberately making your own slightly altered versions of the Amiga music, I'm fine with it but please make it clear that's the case.