This would have been an upgraded version, not a clean install. And I likely used the stand alone upgrade, rather than using the updater.
I tried deleting the GLprogs folder and ran the updater, and was told I needed to download 1.6GB, which is more than my bandwidth can handle at the moment. I do however have all the installation files tucked away exactly for moments like this, so I'll try a clean install momentarily.
And as an aside, this reminded me of a problem I had with Doom 3 RoE that was solved by disabling AA. Thinking this might be an engine problem, I tried disabling AA on TDM, but that did nothing.
Update: A clean install seems to have solved the problem. Doesn't really narrow down what the problem was, but at least there is a solution.