I bought in with W$ last year, I assume it is similar for FPP... alot of info on the website
http://www.pokerstars.com/wsop/faq/ . They just deposit the money into your account, they are unable to register you... I believe it was $8500 they send originally and then they send the other $1500 to your account after you register at the Palms with your tournament reciept from the WSOP.
I don't know who you talked to in Stars support (don't ever e-mail the support@pokerstars address, you can get a much better answer by directing to the appropriate party, in this case
wsop@pokerstars.com or
registrations@pokerstars.com), but there is no way they wouldn't let people use FPP for the WSOP
edit: copied and pasted from website... this is last year though so might be different
11. Can I buy a Main Event package with T$ or FPPs?
Yes, provided you are a Platinum or Supernova VIP.
FPPs - You may use 590,000 FPPs to purchase a seat only package(this does not include hotel accommodation or the cash equivalent). Once your request is processed we will deposit 85% of the value of the buy-in into your PokerStars account in cash. You then register for the event directly with the World Series. When you have done so, you bring proof of your registration to the PokerStars office in Las Vegas and sign our PokerStars World Series Terms & Conditions document. Within 5 business days of your doing that, we will deposit the balance (15%) of the buy-in into your PokerStars account.