There is a bug in 7.x where if you are using multiple layers over the same area, the 2nd or top layer, defeats the lower layer. This only happens with a color adjustment, you can make exposure, contrast, sharpening etc, with no problems.
I have an image where I am wanting to adjust the entire sky. I will add a local adjustment layer, with the brush for the entire sky, make a color selection in the blue, and work hue sat, etc. This effects all the area that is masked for the sky. Now in this image, I have a bit of a color cast towards the edge but still in the sky. I don't want adjust all the sky, just the parts with the color cast. Here I would add a 2nd local adjustment layer using the gradient mask. From the upper left corner towards the middle of the image. I should be able to make a color color selection of the blue again and just work on the red cast, however when you make the color adjustment, you lose the part of the 1st mask that is under the gradient mask, it reverts back to the original. This can cause the issue you are seeing, i.e. warmer lighter parts of the image popping back up.
I have noticed this since the beta of 7 and have tried to Phase One's attention it several times. It to me is huge deal on Capture and totally effects one of the main tools, local adjustments/color adjustments. Recently I worked through this issue with Capture Integration and they were easily able to recreate the bug and took it up to Phase One. Phase now "agrees" on the issue of the bug, but as for time line it's anyone's guess.
Basically, once you have masked any part of an image with any of the tools, you cannot make a new layer over the first with any of the tools and make another color selection, as it defeats the layer underneath. You CAN make exposure, contrast, brightness and saturation adjustments to both layers.
Bug is in both Mac and Win versions and on any camera file I have worked with, Canon, Nikon, Fuji, Sony, and Phase One.