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I do not know what happened. But when I rebooted my PC, now Mathematica comes up orange colored. I shut down the PC and tried again, it is still orange. Here is screen shot:

Mathematica graphics

I also did a reset. Holding down the ctrl-shift key. And it is still orange colored

Mathematica graphics

I also deleted C:\Users\<user_name>\AppData\Roaming\Mathematica and started, and it is still orange.

All pop-ups and help now is also orange

Mathematica graphics

Also the little + thing on the start of the cell is orange:

enter image description here

I am not expecting someone to just know the cause of this, but may be someone else had this problem and can suggest what to do.

Windows 7 did large update on my PC last night, so it might have something to do with it, not sure. Here is the list of the updates

enter image description here

I did not do anything to Mathematica itself or change anything configuration with it. I just turned orange. No other app I am using has turned orange as well.

specs: Version 10.1, 64 bits, windows 7, 64 bits.

Update

I found something interesting: When I take image of the cell using SEUploader, then it comes up in the image with orange background. While in the notebook itself, it is still white. So SEPloader is picking up the orange color from somewhere. Here is screen shot:

enter image description here

Maybe the above will give a clue to the problem.

per request below, here is the color setting on my PC. I never touch this stuff as I do not understand colors.

enter image description here

But I turned the option above to "use NVIDIA setting" from the "Other applications control color settings" and restarted Mathematica, and it is still orange.

Added result of

FileNames["C:\\Program Files\\Wolfram \
Research\\Mathematica\\10.1\\SystemFiles\\Data\\ICC\\*"]

Mathematica graphics

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    $\begingroup$ Is it just me or do the desktop icons in the background of the first picture look orange as well? That reminds me of what it looked like when a CRT monitor I had was dying. Yuck. I hope your problem is fixed soon. $\endgroup$ – Mr.Wizard♦ Jun 28 '15 at 18:52
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    $\begingroup$ Hey guys you must be kidding, Nasser is showing a screendump. Any problems with a CRT or a plug would not show in a digital image. $\endgroup$ – Sjoerd C. de Vries Jun 28 '15 at 18:57
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    $\begingroup$ What do you get when you evaluate FileNames["C:\\Program Files\\Wolfram Research\\Mathematica\\10.1\\SystemFiles\\Data\\ICC\\*"] ? $\endgroup$ – Sjoerd C. de Vries Jun 28 '15 at 19:23
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    $\begingroup$ @SjoerdC.deVries I just did. I run the control panel->Calibrate color-> and clicked next to all options (did not actually change anything) and then clicked apply. Then I restarted Mathematica. And now the color orange has gone ! and it is now turned back to the way it was. If you like to post this as an answer, so I can accept it. This might be useful if it happens to someone in the future. $\endgroup$ – Nasser Jun 28 '15 at 19:44
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    $\begingroup$ Hmm, this made me think of the f.lux app to aid sleep ... nerdsmagazine.com/apps-like-flux-for-android by reducing the blue component of radiated light from your display. Is this an undocumented feature in MMA? :) $\endgroup$ – image_doctor Jun 28 '15 at 23:15
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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.

Pasted from question:

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:

Mathematica graphics

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:

Mathematica graphics

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    $\begingroup$ This is a very bizarre feature of M10. I encountered the same issue with Windows 8 and recalibrating the display color did the trick. $\endgroup$ – bobthechemist Jun 28 '15 at 20:36
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    $\begingroup$ So, now we have to find out under which circumstances it happens (I have not encountered this yet). $\endgroup$ – Sjoerd C. de Vries Jun 28 '15 at 20:39
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    $\begingroup$ ...and after using this solution, my Mathematica (10.0.2) suddenly needs extra time "Formatting Notebook Contents". A very bizarre bug indeed. $\endgroup$ – bobthechemist Jun 29 '15 at 12:34
  • $\begingroup$ Are you sure it's related? Many people get this message (myself included) though we haven't changed this setting or suffer from the orange bug. $\endgroup$ – Sjoerd C. de Vries Jun 29 '15 at 12:36
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    $\begingroup$ @bobthechemist without a doubt, Mathematica (even version 9, which takes a long time to start) has some odd problems with monitors on Windows 7 and 8. I managed to fix my laptop using the monitor driver replacement suggested elsewhere, but for my multiple-monitor desktop, it made no difference. The same problems are not observed on Windows 2003. Someone surely needs to have a serious look at what the FE is doing here. (Hoping for the best with 10.2!) Thanks to your comment, in the mean time, I will try uncalibrating my color and see if it helps. $\endgroup$ – Oleksandr R. Jun 30 '15 at 0:38

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