As far as I can recall, you have to go there three times.
I'm not certain if this would work, but you could try "ResetInterior WinterholdCollegeArchMageQuarters". You might need to save, exit to the main menu and then reload after entering the command to make it take effect. I don't know for sure if it would work, but it might fix whatever is wrong with the location. If that doesn't help, you could check the wiki page for that quest (http://uesp.net/wiki/Skyrim:Good_Intentions), and use "setstage mg04 [stage number]" to skip the parts where you need to visit the archmage.