Arduino.h and wiring_digital.c problem.

Official Hardware Mega Due
5

Baltasar,

what are you missing is to enable Synchronous Data Output (look at page 646 of SAM3X datasheet for more info on that).
The following snippet of code should solve your issue (warning: totally untested :))

REG_PIOA_OWER = 0xFFFFFFFF;
REG_PIOB_OWER = 0xFFFFFFFF;
REG_PIOC_OWER = 0xFFFFFFFF;

I'm thinking about adding this as a default initialization in Arduino Core.