Dude, I go over my bill with a fine-tooth comb every month and this has not ALWAYS been there. I've had my FAN discount applied the week I got my 3G. Every month I see a 39.99 charge for the rate plan, and 30.00 for data. With my university fan discount, I pay around 62.00 dollars a month (and this is after taxes and other charges, plus an extra 200 monthly minutes from a rate code and free unlimited texting from AT&T messing up my bill a few times), and this is without the "crossed out" portion originally appearing on my bill. I'll come back next month and see if there's a $6.00 difference from my standard bill every month and post it here.
I am guessing the details of your FAN account before (as negotiated between AT&T and your university) did not apply to voice. But now, finally it is. So that must mean AT&T is now allowing your FAN account to be applied on voice, which must have sucked for you before because my FAN account has been giving me a monthly discount on voice and data ever since I got the 3G last year. Better late than never I guess.
You guys might also want to check out if your newly applied discount is also applied on the data portion of your bill.