Found the Problem… On my Pi3 i use a cooling case and a pin header to extend the pins over the case. I started to flash the firmware using sudo GCFFlasher_internal -t 60 -f firmware/deCONZ_Rpi_0x26400500.bin.GCF -x 3 and than slowly move the RaspBee on the pin header. The Output on the console changed and the flasshing starts, i hold the RaspBee in place until SUCCESS.
The Problem was the Connection on the GPIO Header pins! I hope this information helps someone else.