What load are you putting on the machine? if it is highly inductive and has harmonic content, it could cause this, or an unbalanced load with some harmonic content.
What type of load is it? If the load is unbalanced, I guess if you added 3 phase sensing to the machine that might help.

You can get a spare AVR, but if the AVR had failed, you would be getting low voltage on all three phases, so that isn't the problem in my opinion.