Hi,
This wasn't "thumping" as much as pumping woofers. Nothing to do with isolation. I have a very heavy rack that is well isolated and sits on a cement floor. The woofers would pump and move even when nothing was being played (at the begining of records). It wasn't a case of lack of isolation and I tried tons of stuff to make it stop. Since the subsonic filter eliminated the problem, I have to assume it was caused by subsonic noise coming through the speakers. Led me to say "hmmm, that's what that button is for!"
J
Jman,
Was it only when the cartridge was in contact with the record? Or did it happen when the arm was "up"?
The Warp thing is possible, as is the fact that the tracking might be too much for the suspension and the tone arm sets up a bounce (kinda like the guy in first gear who gives the car a little gas, and the car rises up, he lets off the gas, and the car lowers and slows, but this causes him to push on the gas again and it rises up, and the cycle repeats itself)
These types of things can cause some rather large excursions, and the SUBSONIC filters just simply remove (filter) them so they don't affect the sound.
Cartridge suspension, tracking and tone arm matching, can sometimes be very tricky, especially if you have a stiff suspension (no jokes, I've been playing the straight man too much lately

) and a light tone arm.
Also check your VTA to make sure it is correct as it can affect the suspension, if it is way off.