Hmm, do no commands show up under "_Uncategorized"?
The two things you'll want to do is check your groups.txt/users.txt file to see if there are any remaining references to the commands that have been removed. Secondly, there is a file in the ULX data folder called misc_registered.txt which may store references to the removed commands as well- If you don't want to edit it manually, I *think* you should be safe to delete it, but each command may give itself access to its respective default group.
