Have you called VPI? I have this drive and have not had any problems, but it's in an area that it would be difficult to resonate in. Any issues I have had, have been dealt with very promptly and professionally by the people at VPI. If you haven't called them, you should because they are more likely to have seen or heard of this problem before and likely have a solution.
VPI Synchronous Motor Hum problem
I have the above (newer model) and it hum's when I switch it to 45 RPM. It is fine at 33 1/3. What could be the problem?? The unit sits on top of my wood equipment cabinet. In the cabinet and right under the motor drive is my pre-amp. The T/T is off to the side of the cabinet a few feet away. Help!