You really should contact VPI directly about this problem. They are world-class at customer support. If you play your cards right, they may offer to remachine it or replace it or swap it out for an aluminum classic platter. They helped me tremendously last year when the table I bought from used on agon didn't have a motor or SDS last year. HW ended up rebuilding and repainting a show unit for me for only $800, despite the $2200 list price. He even threw in a belt kit and some lube.
Note that although Harry gave control of the business to his son, he seems to haunt the Audio Asylum vinyl pages and seems to swoop down like a guardian angel to solve problems people have with his gear. Good luck with resolving your problems. Due to my owning a SSM machine, I have done quite a bit of research into its configurations. The consensus seems to be that the classic platter perform better with the rim-drive, but that the super platter mates better when using the 2-motor belt-drive option, which I use. As to the machining quality, I checked my super-platter for runout (concentricity) with a dial test indicator reading 1/1000" that I had when I was a toolmaker. Total runout is less than a half a thousandth of an inch on all three layers. If yours left the factory with misalignment greater than that, it should be brought first to VPI's attention.