If a user wants to change their signature, in the UCP/ACP the previous flags are not reused (since they are not stored in the users table of the database) and automatically their global preferences are used. This isn't exactly logical, because if the user wants to disable BBcodes in their signature, they'll want it to /stay/ disabled every time they edit their signature, until they themselves re-enable it.
Simplest way to fix this would be to add a quick user_sig_options field, and not use anything like the posts table and the trio of columns for enable_bbcode/enable_magic_urls/enable_smilies.