(Whoops, I had notifications turned off!)
Hm, thanks. That makes GenTool happier (I get a more complete GenTool menu, and it's now saying "cracked" instead of "incompatible"), but unfortunately the alleged online version mismatch remains. Actually visiting them again for today, and LAN play's still working fine. Odd.
Edit: There's a blur of GenTool's overlay checking files bottom-left, before determining it's a "modified" install. It doesn't care about extra stuff in the folder, does it? I've got the original exe zipped up under there. Does the list of files get logged somewhere?