That sucks bro.
Since you said that you're enrolled in one of the best programs in the State, and not many people make it up to there, maybe they're just trying to verify that you are actually enrolled in that school and the certificates/documents are not forged. if you're legit, there shouldn't be a problem - they'll probably renew your visa in a week or two.

on a different note, (this may not apply to your case but might be useful to other folks on a similar boat) one of my mentors once told me that if you're enrolled in a program like mol bio, immunology, etc, sometimes the DHS folks get freaked out for no reason - they assume that as an international, you can potentially harm the US by developing bioweapons and all that jazz with the knowledge you have. so, i was told not to mention terms like cloning, genetic modification, immunotherapy, etc (either in written or oral form) while conversing with the immigration officers because they'll often hold you from going out or coming in until they do some rigorous background checks and find out everything about you including where you crapped last time.

hope things will get resolved soon. now i'm scared that i might get held up next time i go for renewal