The color space theory was a good one, but actually when I look at the original camera H.264’s and the ProRes files (both pre and post FCP) they all look exactly the same.
Seems that the problem is just the viewer window in FCP with ProRes files; it makes them less saturated with more contrast. I’ve read that the new Final Cut Studio bundle has improved ProRes support, maybe after an upgrade the files will look correct in FCP.
I’m really shocked nobody else has encountered this problem before. We do exclusively web-oriented videos, so external monitors and in depth color correction isn’t necessary. Simple tweaks with 3-Way Color Corrector are more than enough. I just need consistency through the entire process.