High frequency means that the incoming power's frequency was much too high (greater than 69 Hz, if I remember the specs—rather an unusual fault to have, as utility power frequency tolerance is very tight, within a tenth of a Hz (and more accurate long-term) and cannot vary across the AC power grid due to the physics of AC power distribution. Maybe extreme noise on the line would cause the error, or an intermittent connection or something along those lines.
The voltage measurements for the GFCI are not surprising give that it was tripped. Your two 48 V measurements are to an open (floating) circuit. An analog voltmeter (with a lower input impedance) would likely read zero volts, and arguably give a more informative reading in this case.
It sounds like you have a couple of problems (which are possibly related): a ground fault, causing the GFCI to trip, and some fault preventing the second leg from giving power. Since the generator works, it would seem to possibly be in the input cord or the EMS or its wiring.