This is still happening, and I'm not sure why. But, it does seem to be happening ever since I organised level packs into sub-folders.
So, I have put all original levels into one folder, all community packs into another, challenge/contest packs into yet another, and finally my own packs in another.
It's sometimes OK, but sometimes it crashes NeoLemmix. Do I have to make sure they're indexed properly or something, or - will I have to unpack the folders and have them all in a separate list again?