After resetting both Players a couple of times the blinking went away.
The only thing which I can imagine what it could be about is the 'On Air display' but don't know what is indicating it. In the Settings it is activated.
Meanwhile I read the Manual for both the XDJ-1000 and my DJM-900nsx2 but the DJM has no indication to Support on Air Display.
I experienced the blinking the first time when playing around with Trakor Pro.
Any comment is appreciated.