Interesting, shinros - I've never played with Conjuration in vanilla Skyrim so I wasn't sure how it worked. I guess I could be gaining a tiny amount of xp from casting the Flame Atronachs.
As for mods, I am using the excellent Requiem mod, which makes some changes to the perk trees. It grants a perk at skill lvl 50 that allows you to control 2 atronachs, for example. I have that perk, and so I was kind of expecting my Conjuration to shoot through the roof given how many of the FAs I've been summoning.
I'm also casting my FAs waaayyyy out ahead of me, since I have a perk that gives them longer range. In some cases, they're killing stuff before the enemy knows I'm there. So I wonder if that means they're not considered to be "in combat" (since I'm not directly involved, and don't hear the battle music), and as a result aren't getting xp...