I know someone who had a similar situation. So, in March of 2010, after losing a lawsuit that, I believe, was initially filed by the Mayo Clinic, the IRS finally conceded they would honor medical resident FICA refund claims for trainees who had those taxes deducted up to April 1, 2005. The issue had to do with whether trainees were considered "students" or "employees" for tax purposes. Mayo argued they should be considered students and the Treasury argued employees, and, therefore, their wages should be taxable. The Treasury lost, but after April 1, 2005 changed their definition of student such that any trainee working over 40hrs/wk could no longer be considered a student.
To answer your question: though you should have been eligible for a refund given your employment dates prior to 2005, unfortunately, the statute of limitations to file a claim expired several years ago, and you cannot appeal that decision. Most institutions filed claims on their own behalf (for their portion of the FICA taxes) as well as on the trainees behalf, after obtaining their consent. I'm assuming they used last known addresses to track former trainees down, but I'm not sure how they attempted to contact them.
Unfortunately, if you have not received and signed a consent form by now, I doubt there's anything you can do at this point. To be sure, you should contact the GME department of your former training institution and verify that the deadline has passed, but the odds are very slim you will be able to obtain a refund at this point if you have not already been contacted by your former training institution.
As far as the IRS being fair...well...it's the IRS, since when has the IRS been fair. They get to play by their own rules. Your friend must have been in training for quite some time, or had quite a salary to have received that big of a refund, even with statutory interest. Most trainees are probably looking at refunds in the thousands but $17K seems kinda steep. I doubt that many will be looking at numbers like that. Who knows though, too many variables to account for to know for sure.
Sorry to be the bearer of bad news. If you're interested the IRS has a FAQs pertaining to this:
http://www.irs.gov/pub/irs-tege/medresident_fica_qa_10132010.pdf
If it's any consolation, you can take solace in knowing that your Social Security benefits (assuming it'll still be around when you become eligible) won't be lower as a result of having received the FICA refund. Awesome, am I right?