The story continues, when powering the Mega with USB cable or 12V on the DC connector the DS1307 works fine (with the 5sec. delay) I use the regulated 5V output of the Mega to power the DS1307.
On my addon board besides the clock (and some other stuff) I placed a DC-DC regulator that converts up to 24V to 5V, the 5V goes in the VIN of the Mega board.
When using this power supply the DS1307 does not function, however all other hardware (including the Mega) does.
Even setting the delay to stabilize power to 10sec. does not solve this, am I missing something crucial like power drop inside the Mega when feeding with 5V?
The device is used on a car battery (up to 14.5V) so I am afraid to put that in the DC connector of the Mega that is why I choose my own power supply.