Skyrim Good Intentions / Revealing the Unseen Quest Glitch?
According to UESP wiki (and my boyfriend had the same problem with his), if for some reason you accidentally exit out of the conversation with Mirabelle before you talk about the Staff of Magnus, you will be unable to ever have that option again. However, there was supposedly an "unofficial patch" that fixed this.
I'm not sure if these circumstances were the same as yours, but, nevertheless, here's the link and I hope it helps!:
http://www.uesp.net/wiki/Skyrim:Revealing_the_Unseen