Pixhawk 6x

i am using pixhawk 6X with PX4 13.3. the problem i am facing is that when i am giving power from power port 1 only GPS 2 is getting signals and when i am giving from port 2 only GPS 1 is working and when i am giving power from USB both GPS is working fine.

I don’t have such a problem on my Pixhawk 6x
Suspect internal issue within Pixhawk
You could try to bridge the positive wire from one GPS to the other in order to have both working.
Or if the unit is still new you may have to return unit for a warranty claim.