Earth Fault Relay Indiacation

I do not see how your Megger test could be good if you have an earth fault indication, have you tested the complete circuit not just the motor windings?

Its a large motor and would suspect a temperature problem but even so to take one or two hours seems rather a long time to heat up to fault indication, larger motors have larger amounts of metal expansion, did your tests take place when the fault showed up or cant you stop the process at that time or is the fault staying put till the end of the production run, then you are testing?? does the fault come back on immediately if you if you restart after shutdown??

It has to be a problem iether your motor or EFI system aproach the problem methodicly and eliminate section by section.