What kind of hard drive are you using? Often, bottlenecks at the drive cause strange playback behavior. Also, do not rely on what you see in the canvas or viewer. The only way to judge playback is with an external monitor and an I/O card or box of some kind (AJA, Blackmagic, Matrox, etc.). Also, ProRes444 is overkill. ProRes422 should be fine. It places less strain on your processor and hard drive.
John
MacPro 8-core 2.8GHz, 16 GB RAM, OS 10.8.4, QT10.1, Kona 3, Dual Cinema 23, ATI Radeon HD 5870, 24″ TV-Logic Monitor, ATTO ExpressSAS R380 RAID Adapter, PDE enclosure with 8-drive 6TB RAID 5
FCS 3 (FCP 7.0.3, Motion 4.0.3, Comp 3.5.3, DVDSP 4.2.2, Color 1.5.3)
FCP-X 10.0.9, Motion 5.0.7, Compressor 4.0.7
Pro Tools HD 10 w SYNC IO & 192 Digital I/O, Yamaha DM1000, Millennia Media HV-3C, Neumann U87, Schoeps Mk41 mics, Genelec DSP Monitors, Prima CDQ120 ISDN