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.
