I have no clue, especially as there are similar problems in a clean linux environment.

Are you using Beta 1.5.5 or 1.5.5-R2?
I'll do a clean windows install the next couple of days, maybe things behave different then.
Just to make sure, when installing the IDE, is this the correct order for a x64 system?
- Download and install/extract the Arduino beta IDE (1.5.5-R2)
- Install the drivers from the Arduino IDE "drivers" folder (dpinst-amd64.exe)
- Extract the DigiX hardware folder to "Documents\Arduino"
- Run the DigiX "Install Drivers - 64bit.bat" file
- Run the Arduino IDE, select COM Port and Board "Digistump DigiX (standard)", programmer is AVRISP mkII
One thing i noticed, when you go to "<arduino installation folder>\hardware\tools" and run "listComPorts.exe" the program shows all COM ports but then crashes with the following message:

(it shows the DigiX COM port for just a moment after i click the OK button)
Maybe its caused by the german language of my OS? Can anyone confirm that?