This file keeps popping up in a seperate browser and I can't stop it. file:///C:/Program%20Files%20%28x86%29/Mozilla%20Firefox/

My McAffee and Windows Security Essentials have scanned for virus and find nothing. It's acting like a popup opening a seperate browser window.

Try to run firefox from your profile(C:\program files (x86)\ Mozilla Firefox ),If it works then make a shortcut from you profile (C:\program files (x86)\ Mozilla Firefox) and check what happens. (copy and paste it to desktop)
It seems your firefox profiles misplaced from its profile .

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