While yes it's quite annoying that vBulletin added a rule that functions as a catchall and then proceeds to tamper with the query string - and would have similar results, this issue was reported as occurring under vB 3.8. However, that doesn't prevent Hostboard from having other RewriteRules that, if in a particular order, could result in 404 errors when Simple URLs are enabled. To rule this out, I recommend posting the relevant parts of the .htaccess file.
If not that, it's possible the problems here are related in part to the problems that were discovered today with the Island namespace. Basically, if you performed a fresh install with version 2.5.0 or later, OR you performed a database restore since upgrading to 2.5.0 or later and the backup was from after the upgrade, your namespace IDs get reordered and result in pages that have broken URLs or say "There is no text in this page" (NOT fixable by Rebuild All Namespaces).
Whether it's even a contributing factor at all is a good question, but I did visit hostboard.com yesterday and notice some pages that may have been screwed up by this bug.