I had some problems with the avrdude 5.3.1. It complains about reading the fuses properly.
Verify error - unable to read lfuse properly. Programmer may not be reliable.
A workaround is to use the -u switch to override this check. As the new version with this bug fixed is not available for windows, I tried to compile it myself. I used MinGW and MSYS and it worked, at least for me. I can now even omit the -F switch, which I had to use before, as the device signature was not read properly. If you want to try it, here you go.
Download: avrdude 5.4 windows
Please note, that this comes without any warranty and is not completly tested or verified.