I think I have found a fix. Go to the console and type 'setstage MG04'. This will start the next quest after Hitting the books. Completing Under Saarthal after you have done this is optional, just continue the storyline from Good Intentions. It worked on mine, when I got the bug. Under Saarthal will remain in your journakl for a bit, but will complete itself eventually, because as far as the questline is concerned, you passed it. The Eye Of Magnus will not appear in the main hall, for the whole storyline, but dont worry, it re-appears when your with Ancano. Hope this helps everyone :P
