I think there might be a bug when installing to a Non-Default directory. (I posted this message before as "Win2K & Studio4", but that wasn't very descriptive).
Anyways, when I installed to C:\Atmel\Studio4, the program couldn't find the part description files (it listed the directory incorrectly in the status window). I tried finding reference to this in the registry and anywhere in the install directory without success. I then un-installed it and re-installed into the default directory and it now seems to work (for now).
Hope this helps other people,