Have a quick check back … theres been a topic covering these kind of issues here before.
I think the final result was that you should set iTunes preferences to import audio as AIFF, 48 kHz, 16bit, Stereo.
FCP4.5HD does a very poor job (or at least a very inconsistent job) of handling CD audio tracks when you drag them straight from CD to your Scratch Disk …. it may well be that QT Pro does a better job, and certainly the iTunes import method above provides consistently good audio.
Also the much anticipated FCP5 will likely fix a myriad of issues, it might be that this one is amongst them.
Cheers
Andy