I am having this issue a lot in combat when I swap to a favorite spell via hotkey, a lot of times it will only equip the spell in 1 hand and when I hit the same key again to equip the same spell in the other hand half the time it does nothing. The only way I can fix this is to press another hotkey to swap in a weapon or different spell and then try it again...

I thought you could only hotkey things to the off hand with a mod.
I dont use any mods, so I couldnt really say.

Normally I can just hit the same hotkey twice and it will equip the spell in both hands, but for some reason it doesn't always work, specificly in combat

Same thing happens to me. Not every day, more like every other.... more often then not it seems to be a healing spell too. In addition, the game seems to forget my Bow has been set to hot key 6 every few days... When I had two identical swords hot keyed it would drop them frequently.