Glenn,
I don't see how they could possibly blame it in the power Co. A ground fault breaker should be oblivious to what is happening on its line side. My first thoughts while reading this were that the settings were set to low. (time and trip curves) But you say they didn't have the problem until after a lightning storm? Did anyone think that maybe the breaker is doing it's job and they really have a ground fault? You say they meggered the motor but did they megger the feed to the motor. The lightning storm could be purely coincidental and the have a break down in insulation value on the feeds. Maybe a lightning strike caused the break down. All this is speculation but maybe something to try.
Nick