The dreaded "Quicktime gamma bug" that has been identified for several years but not entirely solved. It sucks.
Technically speaking, the gamma bug is due to the use of the +dct8x8 flag in the encode and not erroneous colr nclc atoms in the Quicktime wrapper.
+dct8x8 is DISABLED in main and baseline encoding methods but is ENABLED in high profile settings.
Try FFmpeg.
I found that by using a "high profile" H.264 (in fact, Videolan's x264 codec), the gamma bug went away. Good original colour in Quicktime with or without the Final cut pro compatibility switch.
Check the FFmpeg forum for an installation guide for Mac. It's really not that hard.
http://forums.creativecow.net/ffmpeg
http://forums.creativecow.net/readpost/291/22
I would be happy to supply some command lines to get you started with H.264 Mp4 files if you like.
Michael
"half-way to world domination A.K.A. the belligerent blue bike shed"