Thread: Changing Color
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We've done some work for OmniFocus 1.1 (coming out of sneakypeek soon) that makes stuff like this easier to fix, but my guess is that you're using OmniFocus 1.0.3.

If that's the case, I'd attach the following file to an email to the support ninjas:
<your home folder>/Library/Preferences/com.omnigroup.omnifocus.plist

If you are using OmniFocus 1.1, just open up the Style pane of preferences and hit the Reset button in the lower left corner.