I had the same problem when I got my MacBook in November.
My problem was also with slightly scratched CDs. I went through 3 new MacBooks, and all of them had the same problem, so I figured, whatever, I will just live with it.
I have dealt with the problem, up until today however. The Firware Update completely fixed the problem for me. However, I see that it did not do a lot of good for some people. I had just completely reformated my HD yesterday, so everthing was nice and fresh when I installed it.
Maybe that had something to do with it...