HDMI Port, Wrong Color Space, Here MIGHT be the best solution.
So, I've been searching the forums, and couldn't find the solution. Today I finally found the fix.
I had been trying to find a solution to this problem where a monitor is attached to HDMI and the Mac Mini [late 2012, 6,2] thinks it is a television and uses the wrong color space.
Doing some google-fu, I stumble across this site:
I followed the fix, and bingo.. I can look at my monitor again without my eyes bleeding.
Thanks ireckon.net, you saved me.
PS... if this solution has already been found, Forgive the double post. It seems a lot of people are still looking for it.
Mac mini, OS X Mountain Lion (10.8.2), Dual Monitor, Dual HDMI