In either the Display or the Color Management control panel navigate to the calibration option and change some settings and revert back. Click Apply to see if it helps.
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Problem resolved. Thanks to suggestion by SjoerdC.deVries in comments. I run the windows color calibration and clicked apply, then restarted Mathematica, and now the orange color has gone:
It looks like the windows 7 monitor updates caused Mathematica to get little confused. Running windows control panel->Calibrate color->Apply fixed whatever the problem was. Here is the button to click on:
