First I've heard this.
I had a 30HP 480v motor a couple years ago, throwing ground faults on pf700. Megged everything like usual at 1000vdc, and it didn't show any issues. Checked motor connections, the usual. I couldn't figure it out.
I finally had enough and mentioned to the customer that if the motor was important enough, he ought to have a spare. A spare that I wanted to use for troubleshooting purposes also. They bought one and installed it. Drive started up and ran it just fine.
I was told at the time by the motor shop that meggers can't pick things up as well as a drive can. After going through this, I believe it. That was the only motor in 10 years of megging, that the megger wasn't able to pick up the ground fault but the drive could. Fluke 1507, which is the same you use, I believe.
So, once in 10 years, I'm still not sure that's worth picking up a 1500v megger for that rare of an instance.
My personal drive battle right now is with a 200HP PF400 throwing overvoltage, drive overload, heatsink overtemp, etc codes. Right now I think the heat is making it wacky, we're going to try leaving the enclosure doors open and pointing a fan at it. So I feel your pain chasing drive/motor gremlins.