Create a System.dat and save it. Then open it again, remove some of the levels and save the System.dat again. Built a .nxp now. Big surprise: The deleted levels are contained in the .nxp!
The reason seems to be, that the deleted levels (in the toolkit) got not get deleted in the levels subdirectory when saving the modified System.dat. Thus the toolkit finds them when building the .nxp and adds them.
When these level files are deleted manually, the .nxp contains once again the correct levels.
I noticed this a while ago but forgot to fix it. I'll try and get a fix out later today.
Well shit. Seems I forgot about this one altogether. But since I'm working on the toolkit right now, it's a good time to fix this up. :)
EDIT: Well. It seems I already fixed this in the code, I just never released the fix.
Seems the fix wasn't quite right, and this bug is still occuring. So I've reopened this one and moved it back to the main board.
Alright. Got it fixed for real this time. :)