I recommend contacting Wolfram Technical Support about this problem. I'm fairly certain they've seen this issue before.
That said, you probably can solve the problem by following this article: http://support.wolfram.com/kb/12464. In particular, you want to remove the files:
- C:\ProgramData\Mathematica
- C:\Users\YourUserNameOnTheComputer\AppData\Roaming\Mathematica
This should reset Mathematica so to speak. When you start Mathematica you'll be asked for your activiation key. Again, if you have any problems beyond this, definitely contact Wolfram Technical Support.
http://www.wolfram.com/support/contact/