How are you monitoring your program? It’s not clear what the frame rate is of the problem movies. If they are 29.97 in a 23.98 timeline, that’s probably where the stuttering comes from. Also, particularly in AfterFX, make sure the frame rate is 23.976 NOT 23.98. 23.98 is shorthand for 23.976. When FCP says 23.98 it means 23.976. When AfterFX says 23.98 it means that literally, and that file will be funky in a 23.976 timeline in FCP.
John
MacPro 8-core 2.8GHz 8 GB RAM OS 10.5.8 QT7.6.4 Kona 3 Dual Cinema 23 ATI Radeon HD 3870, 24″ TV-Logic Monitor, ATTO ExpressSAS R380 RAID Adapter, PDE enclosure with 8-drive 6TB RAID 5
FCS 3 (FCP 7.0.1, Motion 4.0.1, Comp 3.5.1, DVDSP 4.2.2, Color 1.5.1)
Pro Tools HD w SYNC IO, Yamaha DM1000, Millennia Media HV-3C, Neumann U87, Schoeps Mk41 mics, Genelec Monitors, PrimaLT ISDN