I'm not sure if an AC leakage clamp meter will show much, especially if the issue is high frequency based or chopped or distorted waveform/s via cabling bleed kicking all over the shop
There may even be a freaky DC component in there too
Even the better big dollar AC clamp meters might extend from 2khz and stretch to 10khz,
most roll off at 500hz to 2k, they are really geared for 50/60/400hz apps afaik
A cable break current measurement with a 100khz AC bandwidth multimeter might be a better way to go,
even a Fluke 87V may not cut it, it rolls off at 14 to 20khz and your issues may be at 40 to 70 khz
The transformer is obviously killing off the generated leakage nasties because it's a LF device for starters, coupled with the isolation/magnetic/air decoupling factor
Not sure how a generator would cope with such a VFD load btw, especially if the gen has onboard regulator and cutoff electronics, so 'try before you buy'
If you don't find an issue with the VFD itself or a safe workaround, I'd be going the way I do it for -temperamental- devices
I plug them into a properly rated isolation transformer with FULL ground/earthing on the input and output and the metal box chassis and transformer body,
and check that the central earth/ground bonding point isn't a halfassed job done with flimsy washers/screws/bolts,
squashed on to the paint or powder coating
by some Friday afternoon manufacturing process from across the the ocean... and transformer OUTPUT neutral and earth ground tied together
Most MIS-LABELED so called 'isolation transformers' come wired this way anyway, aka 'medical isolation transformer' labels etc
so all you have to do is open the box and verify for yourself visually
and or do it the easy way with a good multimeter on Ohms continuity check (not buzzer) if the box is rivetted/pita to get into.
Naturally you do all this with the tranny in the ON position and disconnected from the death mains!
Basically if the earth/ground reads ok everywhere expected, and the transformer neutral and earth/ground read as connected 'zero ohms',
you should be good to go and 100% legit,
no DIY hackery or isolation guesswork and prayer required
With a transformer wired this way you also have the option (recommended) to plug the VFD into a portable RCD/GFCI (and maybe a MCB too) and into the transformers output,
and if it trips due to a mishap, your earth leakage device upstream at the switchboard won't know or care
You can also use the TEST button on the portable RCD/GFCI to ensure the function works
otherwise... it's oscilloscope time, with all the pita 'proper procedures' to suss out safely wth is going on where...
without taking out the scope
or zapping the already frustrated VFD owner...