since it looks for me like a new topic I continue http://arduino.cc/forum/index.php/topic,58650.0.html here.
The same problem can be reproduced with a common power supply.
The DCF77 does not get a clean signal, when attached to the power connector. The code is tested on the USB connection and random runs make a red light flash permanently when the signal is locked, which is the change for testing this setup:
Is there a DIR (Do it right) for grounding the arduino in an independent setup to get the jitter away?