hey scott, is this not a pure vf drive unit but a early type of dc injection unit, or similar, for slow down and stop? a normal vf unit does this in 1 with the regeneration resitor on the side.
i would say it sounds like the supply was not quite the same as the normal supply ie like there was a dc supply on a ac circuit.if your using a seperate braking unit i wound be looking into somehow it got a back feed to fwd bias the diodes on the braking unit.
im spitballing here.