mattallen37:
I'm not entirely sure what I'm supposed to do to fix the problem.I ran the command prompt line you posted (after filling in the WinAVR bin location). It seems to have removed the directory "C:\Program Files (x86)\Arduino\Arduino ERW 1.0.1i\hardware\tools\avr\bin" from that registry key I mentioned earlier, but it doesn't seem to help any more than me manually removing it.
Right, but I am not sure what is your problem really. You have a newer version of WinAVR? because having the path for C:\Program Files (x86)\Arduino\Arduino ERW... set means you can use WinAVR from any command prompt without having to install it again.