Seems the reply to almost every forum anywhere is always "use something else" (which never actually answers the question), I'll reply to myself in case anyone in the future needs help.
I'm no sysadmin, but I did a search through the system of everywhere there are tex, texlive and latex things installed. It ended up being that our /usr/share/texlive directory had discrepancies and the settings for TeX notation in moodle showed where various executables should be installed, but those were also missing. Our sysadmin figured out how to get those items installed. Installing packages can be tricky, apparently, making sure they get all the parts. I'm just glad he fixed it.
The way I was able to test this was to export a course with some math formulas, then import it into the new system. That generated the image with the same hash in the filter/tex dir in the moodle filesystem. They were a different size, different bytes and the physical appearance was bigger. Once the sysadmin got the packages installed correctly, I deleted the images so they'd be regenerated and voila! It was fixed.