Steps to reproduce:
1. Make a level file.
2. Edit the level by hand to specify a music with a path. EG: "Lemmings_Plus_V/abstract1".
3. Load the level in the editor. Note that the music input box still contains the path at this point. (You can also just type in such a name, rather than loading a level that already has one - the point of mentioning this is to show that loading does not trigger the bug, only saving.)
4. Save the level.
5. Re-load the saved level file, or examine it in a text editor. Notice that the path has been stripped (eg. "Lemmings_Plus_V/abstract1" will just become "abstract1").
Note that NeoLemmix itself is completely capable of handling such names.
I remember the pack toolkit also having this bug somewhere, although looking at it now, I can't seem to find any indication it has the bug, nor that there's even anything that would likely trigger the bug. Maybe I'm just remembering wrong.
Fixed for the next editor version.