Try exporting a self-contained or reference movie from FCP. Then, drag that into Compressor and go from there. Export Using Compressor doesn’t always work as expected.
Also, try trashing prefs, repairing permissions and run Disk Warrior. If you don’t own it, buy it. It’s an indispensable program.
John
MacPro 8-core 2.8GHz 8 GB RAM OS 10.5.5 QT7.5.5 Kona 3 Dual Cinema 23 ATI Radeon HD 3870
ATTO ExpressSAS R380 RAID Adapter, PDE Enclosure with 8-drive 6TB RAID 5
24″ TV-Logic Monitor
Final Cut Studio 2 (up to date)
Pro Tools HD w SYNC IO, Yamaha DM1000, Millennia Media HV-3C, Neumann U87, Schoeps Mk41 mics, Genelec Monitors, PrimaLT ISDN