Problem
Very strange permissions issues in vBulletin.
Solution
Rebuild the bitfields by going to /admincp/index.php?do=buildbitfields
Discussion
On a new board that I was configuring, it somehow got into a weird state where the users in the Administrator usergroup had missing moderation options. In the Moderation pulldown (and in the Thread Tools pulldown), only a few of the moderation action choices were available.
I was pretty damn sure it was not a configuration issue, having triple- and quadruple-checked permissions, and creating test users from scratch. I was going crazy with frustration until I ran into this forum post that introduced me to rebuilding bitfields. Bitfields are rebuilt when products are added or removed. Sometimes the process doesn't work perfectly.
So if you run into a crazy permissions issue that you're pretty darn sure is not a misconfiguration, try rebuilding the bitfields.
(This was for VB ver. 3.6.8)