I’m not sure why you are experiencing the color shift, etc. I don’t use the suggested workflow in the Ken Stone article. Instead, I first export using File>Export QT movie>Use current settings. Do not check Recompress Frames and it can be either a Self-Contained Movie or ref movie (uncheck make self-contained). At this point you can open the exported file to see what it looks like in QT Player. If you like what you see use Compressor to make the h.264 movie. Compressor will do a much better job compared to QT Pro, although, it will take time. Be sure to choose the Best settings in all places in the Encoder tab of the Inspector (in Compressor).
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