That's a very interesting problem. This quote from the link you posted
sums it up "A normal ac power supply is symmetrical, so that its
three-phase vectors sum to zero. But variable frequency drives turn that
into dc current, and then chop it into power at rates to 20 kHz. At
those high frequencies, constant, perfect phase balance is impossible ‹
and the phase vectors sum to a nonzero voltage."

There still could be an solution in the controller that could balance
the fields and eliminate the shaft currents but you might end up losing
some of the efficiency.

There are always very slight differences in each phase of a three
phase winding, and the currents are always slightly different, even if
the supply is symmetrical. One of the tests for winding integrity for
new and in service motors is to place different frequency voltages on
the three phases and compare the current waveforms. They will be
slightly different, but the differences can be indications of where
problems are.

The circulating currents caused by the differences have only been an
issue in the past with larger (say over 300-500 HP) motors. Now, with
these nasty waveforms, the problem shows up in much lower HP.

This is only one of the motor problems with these drives. I'm sure
manufacturers have changed and are continuing to change their designs
to handle the added voltage stresses and heating problems caused by
these drives as well.

Similar "growing problems" occurred in the 60's-80's when industry
changed from DC drives that used DC generators to solid state DC
drives.

Bob