...I've never run into any sort of problem like this before, and I've heard all the (quite valid) complaints about the latest DB version's bugs. I've run DB on the school computers before, and I've never run into any sort of problem like that.
Then again, my school isn't exactly what you'd call secure.
You say it happens after you test it a few times?
Make sure tempmap.wad isn't read-only, like they say. Testing the map temporarily saves it to the aptly named tempmap.wad, and something might be happening to it. If it only does it when you test, just test the old fashioned way, by saving the map itself and running SRB2.