@combaindeft
B) is clear, since the 3.3 regulator is on the FiPy device. Without that, no power at the 3.3V pin.
Due to A) with the rock solid supply through a battery it is hard to accept, that it's a firmware issue, at least of the FiPy. Still, the PyTrack board can be the culprit. Did you try to run the FiPy without the PyTrack board, like on a breadboard with a separate USB/serial interface?
Shorting 3.3 and GND should be avoided.
P.S.: It's a pity that Pycom does not publish schematics.