I have had major problems using my AVR Tools (STK500, AVRISP and AVRJTAG) with my main computer. This is an AMD 2200+ machine with RAID 1,2 (Striped mirrored drives) and 1Gb ram. Operating system is Windows 2000 Service pack 3. Every time I tried to connect to one of the AVR tools, AVR Studio just hung. I am using AVR Studio version 4.07
Atmel have been looking at the problem for me and we now have a solution.
In registry, locate HKEY_CURRENT_USER\Software\Atmel\AVRTools\STK500\COMPort and set the variable 'Port' to for example 'COM1' in stead of 'Auto'.
In my case, because the connection had never been made, there was no such entry in the registry so I manually added it and now all works well. The auto Com Port selection does not work on my machine. If I select this, I have to go back into the registry to reset it.
There is a new .dll coming out as well that may help some such problems. I am using this here.