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.