deleted every mod, verified the game, even tried uninstalling and reinstalling. The bug is persisting on every one of my saves. At this point I am going to have to delete every save I have and just start over. -_-
I feel like the bug started the second I acquired the dual-cast Axii ability in the Signs tree. I would respect using a potion of Clearance, and the game would still think I had the ability equipped when I used Axii in combat. Which may have something to do with the effect of Axii being completely gimped. The ability even states that 50% of its effectiveness would remain in effect. Just a shame the effect appears to be permanent, with, or without the ability itself.
This seems to be a vanilla issue that crops up from time to time, but I don't think a cause has ever been found. Sometimes, it's a matter of the input device (certain gamepads, especially) not cooperating with the game. It's feasible that other devices, K+M too, might encounter the same type of issue.
I've personally fiddled with it using my K+M, a Logitech gamepad, and an official Xbox 360 gamepad, and I've never been able to create the problem on my end.
Another thing to note is that if you're in an NG+ playthrough, many of the game's mechanics begin breaking down as you reach levels 85+. Rats that can kill you in one hit, enemies that are completely immune to secondary effects, etc. The game was not originally designed to be played at those levels, so there was only so much balancing that could be done. If that's the case, there's nothing for it -- especially if the game has been modded on top of it.
And, of course, the mods. Removing mods can still leave changes in the save-state that cannot be undone. Removing them can leave empty / conflicting reference data that
creates issues, actually. The more mods you're using at once, the greater the chance of borking something if you remove or change anything.
How long have you been going on this particular playthrough?