Is this a machine made by Continental Biomass Industries, a company founded by Anders Ragnarsson and now owned by Terex?
Pretty neat machines really. They make a typical forestry mulcher look like a residential lawnmower. It can be somewhat satisfying when you done balancing one, sort of like taming a wild horse. Have you heard the term "Horse Whisperer"?
From your description, don't discount the possibility your machine might have a cracked, or broken rotor shaft. I've come across one machine that was abused since birth, where it's operators fed it demolition materials it was not designed to eat. The abuse had eventually broken the rotor shaft, which I believe is held in place by use of a Ringfeder device.
I believe it was the infamous Dan Timberlake (yes, "Doctor Dan") along myself (whom at the time was probably of little assistance), balanced the very first CBI machine manufactured in the early 90's.