First, The Pixhawk depends upon voltage/current translation from the power module, using a scaling which can vary (normally) over temperature and the specifics of your hardware.
Before you give up, measure your battery voltage by hand (preferably at the terminals leading into the power module, while the battery is connected), and then make sure the "voltage divider" setting in Power Setup (QSG) is correct: press [Calculate], plug in the value you measured, and then press [Calculate] again.
Second, I've noticed PX4 getting increasingly fussy about having a solid 5.3VDC+ supply at the power port of the FMU itself. This is IMPORTANT, because if you feed it just the typical 5VDC from a BEC that isn't APM/PX4-aware, then the onboard regulators are in dropout. This is a bad situation to fly in.
When Pixhawk's regulators are in dropout, ALL your downstream devices (anything powered from a Pixhawk port) get an unstable supply level---making them unpredictably (but predictably) VERY unhappy.
Unfortunately, all Pixhawk-clone hardware really NEEDS a 5.3VDC+ source supply, as far as I can tell. And since so many PDB/BEC combinations use switching buck regulators, they aren't easily adjusted upwards from their 5VDC factory setting.
I've given up using anything but true, APM/PX4-aware power modules for just this reason. It sucks, because there aren't many PDB/BEC-style ones available. And the newer, Hall-Effect ones are physically, inconveniently large.