I was looking at this the other day....
I think Kurt's table is correct.
If you scroll down further on that Spark Fun webpage, there is the larger complete pin out table for the MicroMod connector which does match Kurt's pin out. This also...
There's an option in the settings on the Digitakt to set it's USB out to Midi Only:
System>>USB config
You could try that if you haven't already. Think by default it's set to Audio/Midi