I got a call from a friend who had some trouble with Traktor Pro 2 and CD timecode. He had no trouble with Vinyl, but once he used CD there was some problems with the Timecode. The symptomes was that transport mode changed from relative to internal playback.
The reason to this was very simple, but took some time to figure out. After trying to calibrate the decks and getting: Unkown medium I figured that it had something to do with the signal. The soundcard input was sat to Phono and the line signal from the CD players resulted in a way to high signal on the input channels.
Solution: Change the input type to Line instead of Phono.