I know it has been a while since you posted but I thought I would reply with my fix anyways to help others like me. After scowering the web for a fix to this exact problem, I have found that the solution in my case is simple.
Color (and all Final Cut for that matter) HATES ICC profile version 4 and only works with version 2. I assume you are running a version 4 profile so just revert to any older version 2, such as the ones from apple or recalibrate under version 2 specs, then restart Color.
I am using a late 2009 imac 27″ dual monitor setup. Never had an issue with Color until I updated to Mountain Lion and got a flickering strobe effect. Then upgraded to Color 1.5.3 and that fixed the strobing issue.
Then I calibrated using an Xrite Eye One Display and i1Profiler Lion edition today under ICC ver 4 and all hell broke loose!
Spread the word and stay away from ICC version 4 if you use Color!