How to fix inverted color on one thunderbolt monitor with maximum resolution set?
The following seems to have fixed it:

sudo mv /Library/Preferences/com.apple.windowserver.plist ~/Desktop/
sudo mv /Users/kbrandt/Library/Preferences/ByHost/com.apple.windowserver.CDE1EF8A-5D17-5A4E-AFB8-C4D1E19616DD.plist ~/


Followed by a reboot. I expect there may be a more targeted way to fix this, but this worked for now.

If you can forgive a little rant, I also have to killall Dock to get the wallpaper on the second monitor, and use SwitchResX to get the monitor to display the proper resolution. In short, it seems OS X sucks with multiple monitors (at least with non-apple displays).