This appears to be a known bug in our version of the search system we use - it has supposedly been fixed in the latest version, though it will cost us $25 to upgrade because this add-on is not free.
I don't think I'm dealing with quite the same pressures though, at the very least its a significantly smaller system. For the time being I'm just going to put together a quick scrubby box though and hope it works good enough to not make my house toxic
I do know this - xenforo dropped the ball by not keeping the vbulletin reputation comments as a feature. The loss of the Reputation comments data when we switched to Xenforo really was the death knell for the site when it came to all the users that left. I know I missed it so much and I got way less interested in the site when that feature was gone and I run the site.