Googling around a bit, I found that installing the mod mentioned in http://www.gamepur.com/news/6332-new-skyrim-mod-fix-no-resistance-bug.html article did indeed fix resistances for me, at least when using fire spells on my summoned flame astronarch. The mod is just an early version of the Skyrim script extender, but for some reason using it seems to fix resistances after the 1.2 patch. Download link for the mod is in that article, enjoy.

I thought that Atronachs maintained their resistances, anyway. It was the player with the problem.

Nope astronarchs too, tested it.

Nope, Atronachs do not have their resistance.