Good catch, TJ.

See, the problem is that I have no way of knowing what templates and files were modified (and how) without doing a side-by-side compare. So everytime an issue pops up that's what I have to do. Okay, this seems to fix it (I'll update the text file in the OP next):
open
/forum/search.php
find the first instance of:
PHP Code:
AND ", $postQueryLogic) . "
add, after:
PHP Code:
" . iif($bbuserinfo['ignoredthreads'], "AND post.threadid NOT IN($bbuserinfo[ignoredthreads])") . "
find:
PHP Code:
ORDER BY lastpost DESC
add, before:
PHP Code:
" . iif($bbuserinfo['ignoredthreads'], "AND threadid NOT IN($bbuserinfo[ignoredthreads])") . "