I have Diggle Gods and YHtNtEP, but not Wizards and I use Steam. Killing major Toms were always crashing my games and that was a real problem when the save games were being corrupted and I couldn't go downstairs. Now that that is fixed, I just go back to the last Autosave, so its not too bad. But it still happening sporadically with both "normal" Major Toms and Inconsequential quest monsters with names.
Have you ever seen him drop the Aethernaut's Helm? Because he's supposed to drop it 75% of the time which could account for it, since both special monster versions of him and the regular one would trigger it. (I don't know what the issue would be though but. Yeah.)
Doesn't appear to be a problem of a dependency with expansions -- well, at least from perusing the XML.
Dredmorpedia has both Major Tom and the Aethernaut's Helm listed as RotDG items. So, if we assume Dredmorpedia is correct, that shouldn't be a problem unless your installation is corrupted. I'd recommend reinstalling and verifying the integrity of your game cache. If you still have the bug after that, then it could be that the Aethernaut's Helm has been misfiled as a CotW item.
I'll try it again, but it happened both before and after the last re-install I tried to fix the bronze discs not being checked in recipes
