[Acenoid]

Meek maybe try to move topics away from them to delete it, maybe try to add a topic and move it away again. Attempt to remove sections / settings in the custom category.

Personally I think that custom categories are no problem ( for me at the moment ).
In case it would no longer synch I would annoy LWD with mails until they fix it. Can't be that hard to provide you with information on how to prove a debug report or smth to thelp them locate the problem :/

Anyways, unless you go public with your realm and unless you want to import stuff from the content market I would recommend you to create custom categories whereever you feel that you need them.

Be sure to update to the latest version, before doing anything.