I have fixed the category bugs reported earlier this week. Please reinstall, as there is also a template fix.
To confirm - if you had left the default permissions forumid as -999 and you edited a category without selecting another forum, then the category would disappear into the big blue yonder.
If you have encountered this problem, you can repair it by running the sql query given by Zhin Jio.
PHP Code:
UPDATE local_linkscat SET catforum=-999 WHERE catforum=0;