For those that have been waiting eagerly, the new USB installer is now making its way through the pipes and should be awailable on gallery.atmel.com in day or so. For those that can't wait, I have sneaked it up to distribute.atmel.no as well. The new version without the windows 8 issues are from the 7.0 series, where the older installer was in the 6.2 series.
The 7.0 installer should upgrade the older installer seamlessly. The troublesome 16-bit error during driver registration is replaced with the DifxApp extension to the WiX system.
The installer has been tested on Windows XP up to Windows 10 without issues. Strong signing is now used, so the security popups should now be reduced (1 for jungo, 1 for Atmel on windows 7, less on other versions). Install speed has increased on most platforms, although Windows XP is still slow. This is due to issues in the authenticode system in XP, which is triggered for each inf file we register.
If you have issues, run the installer with a '/log log.txt' argument and attach the log files that are generated (1 called log.txt, and 1 txt file for each sub-installer, i.e jungo, segger,libusb,winusb and atmel).