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Have you done the 'expert' colour calibration in the display control panel?

I couldn't find the menu option (I can select color profiles and/or make my own by adjusting the RGB settings as needed, but I didn't see anything about "expert" color calibration). However, completely ignoring the apple display calibrator recommendations for contrast and brightness (setting it to what I felt was the rest of osx looked like), adjusting everything else according to the apple calibration app, and tweaking a bunch of smaller areas in my display settings I came up with what's proving to be a pretty decent profile.
 
I couldn't find the menu option (I can select color profiles and/or make my own by adjusting the RGB settings as needed, but I didn't see anything about "expert" color calibration). However, completely ignoring the apple display calibrator recommendations for contrast and brightness (setting it to what I felt was the rest of osx looked like), adjusting everything else according to the apple calibration app, and tweaking a bunch of smaller areas in my display settings I came up with what's proving to be a pretty decent profile.

Sounds like you have a solution.

If you want to try the expert mode, it's a checkbox on the first screen of the calibration wizard when you click the 'Calibrate...' button in the Color/Display panel.
 
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