I've seen references to this online, and now I have it too.

It's simple: favorite Lightning Bolt. Try to equip it. You can only put it on the L hand -- never the R. Switch them around, M1, M2, etc -- it doesn't matter.

How do you get around this?

Click it with the left mouse button, then the right mouse button. Problem solved.

Trust me, I've tried that. It doesn't work.

Then I"m not sure because it always works for me and I'm on PC.

You didn't forget to unlock the Dual Casting perk did you? After playing a mage with dual casting for over 100 hours I made a new character. I kept trying to dual cast like a moron. Then I suddenly remembered that I needed the perk to do so. LOL! Thats what I get for staying up until 3:00am.

I have this same issue only with my Daedric swords. They worked fine favorited until I upgraded them, now I can only equip one through the favorite menu. The click left and right stopped working.

Each time to equip them in both hands I have to go to the item menu and click them both. I tried unfavoriting, and refavoriting again, but it did not help.

Well, you don't need dual cast in order to simply equip a spell in each hand. You only need dual cast to simultaneously cast an overpowered version of a spell.

Ah... Yes. I should read before posting.