Ever since 1.0 I've always had problems with FCP dropping frames when it was playing back video on an NTSC monitor and in the canvas window at the same time. You can disable this in the Audio/Video settings window in the application menu.
However, since I have been only running OS X and FCP 3.0 for only a few weeks on 10.2, I haven't really seen any drop frame issues, also keep in mind that I was running FCP 1, 2, and 3.0 on a 400mhz G4 with 384mb of ram on OS 9.2 (I'm now on a dual 1.42ghz)
Just a thought, but I doubt this might be the problem. You can try turning off the "Put hard disk to sleep whenever possible" in the Energy preference pane.