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.