A thought: when you're playing levels from a subfolder, maybe JJ2 should only look for .j2l files in that specific folder, rather than also check your main JJ2 folder and anything in the AdditionalFileFolders list in plus.ini.

I say this because I was playing Far Away Labs, B2.j2l, in its own folder, but its next level setting is B3, so it cycled to the full level pack, which I had installed in some other folder. Sure, in this case they did happen to be the levels that were supposed to follow B2, but I was only planning on playing one level in that session.