Seems to me that it’s the old quicktime gamma bug with RGB footage. If you capture ProRes 444 I would advise you to duplicate the Kona setup, change the setting in the advance button where it says gamma correction to “none”.
What it does is it tells FCP that your captured file has a RGB gamma 2.22, which, I assume, is the tape gamma. If you don’t do it QT will think the file is 1.8 and it will apply a gamma correction in FCP, causing the gamma shift.
Do a test and see if it helps, that basically solved all my issues with gamma shifts in FCP. I have not captured files as Uncompressed since the release of the ProRes, but if you need to, trying changing the setting in the User preferences>Editing tab where it says “Imported Stills/RGB Video gamma” to 2.22.