Fire atronachs are weak anyway, but trolls are supposed to have quite a bunch of HP. Furthermore, maybe the bug didn't only remove positive resistance but removed the weakness to fire as well. That would mean trolls can eat more fire than they should. Without the bonuses, negative or posite, it's all up to the absolute HP and all manner of beasts and tougher NPCs beat the human player at that.
Btw, has anybody paid attention to what degree general magic resistance can compete with elemental resistance? If it can, does it also protect from dragons' breath attacks (or shouts in general)? In Oblivion elemental resistance protected from that particular elemental attack and also raised the general AC, whereas magic resistance protected from all elemental and other hostile magic but didn't affect the AC. I'm pretty sure in Skyrim elemental resistance does nothing to the AC, though, which naturally would weaken it compared to magic resistance if the latter is still universal.