It sounds like a bug?
I had this issue but not with the spell level window - with the "throw" window. If I didn't choose to throw something, the window just wouldn't close, and sat over the top of my other skills. It did close eventually.
Yeah I'm thinking it's a bug for sure now, I'm going to try reinstalling the mods (I've only got three) and see if that changes anything. Though when you say 'eventually' - what do you mean? Do you mean you mean the windows closed after a few minutes, or that you went back to the game one day and the problem was gone?
