The current imbalance you measured with the clamp meter concerns me. I understand that measurement errors occur with VFD output signals, but I have not seen that level of imbalance when using a Fluke ammeter with a VFD. I normally see readings that are within 10% of what the drive reports.
Is the extruder in a bind? Can you (be safe 1st) turn the machinery input shaft easily?
I would double check the wiring between the drive all the way through the motor. If that checks out good, use a megger (disconnect the leads from the drive first) to check the motor circuit including the leads for problems. Ohm the motor circuit and see if you get balanced readings on all 3 phases. If that all comes back normal, i'd have to see all the motor data and more info about the load.
I have seen hard to start loads cause drives to stall and over-amp at low speeds prior to tuning and usually static tuning is good enough to straighten that out. When I have seen this is was with unusual loads like a loaded incline conveyor belt with little gear reduction...