I was delighted to find when setting up a new AVR development station under Windows 7 that WinAVR has been updated with all the latest components, including avrdude 5.8 with configuration file for all the Xmega chips. There's also an avr32 compiler and toolchain. The new version drops into the latest AVRStudio 4.18 with little fuss.
WinAVR available from sourceforge:
So far no issues.