I'm gonna bet that you didn't bed in your brake pads. This is the procedure I use but most are similar. Reading up on how and why might give you some confidence in doing it too.
http://www.zeckhausen.com/bedding_in_brakes.htm
I'm guessing it's not squeeling because the brakes are hot though. I know mine always make noise after I get them real hot (like at the track) and then go back to normal braking. I think it's due to the pad compound though and it goes away after a little bit.