My apologies for being so inarticulate. Using the 3 Way Color Corrector in FCP7, just to do some very basic things like slightly raise the mids, drop the black levels a little, anything but changing the saturation or hue immediately creates gaps in the histogram.
I've never had this happen in 4:2:2 before. The sequence settings are correct, I am pulling the footage directly from the SSD (as .mov's) via SATA cable.
I am baffled.