Yeah, the 301ing could be creating an issue. Google Webmaster Tools really isn't good at following through redirect paths. After hearing that, and reading everything that Matt researched, it's probably worth reaching out to your .edu partners and asking them to update their links to the proper URL for your site (including if it's https now!).
Also, forgive me if I just missed your answer, but have you set up an https profile of your site in Google Webmaster Tools? Google absolutely distinguishes between the two - my site upgraded about a year ago, and I watched traffic drop in one and jump in the other. I keep both now to monitor inbound links that are to either. It's worthwhile creating a profile with and without www as well.