Ok, I can verify the problem is not with the numbering. I opened CC-0 with FLE, added and applied a new category to one furniture entry, saved it with the same path name, opened the modified .properties file and verified the category for that entry was indeed changed, opened the SH3F file in SH3D, and saw that the new category was not applied. IOW, I replicated ninja's problem.

Doing further testing....