Solved!
My user variable path was, for whatever reason, %CommonProgramFiles%\Microsoft Shared\Windows Live
I changed it to
%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\
And now it’s working again, well not Farcry 3 but that may have not worked beforehand now that I think about it. And Eclipse still works, not to mention for the first time in a while I can run cmd commands without directing it to Sys32.
Thank you for the help everyone it did point me in the right direction.