Raul's suggestion that the cantilever suspension is failing could be an explanation, but the problem I have with that is the cartridge must be pretty new so this seems really unlikely.
I looked at the specs of the ARC used in the review; it cuts off at 10Hz. Your preamp, if still the Io, is only specced to 20Hz (at which point its within 0.25db, suggesting that it can go down considerably further). So its an unknown as to whether that's an influence. Your amps are full power to 1 Hz. I use similar amps in my system at home, but I don't get the woofer pumping, although that was a problem when using the SME5 and has not come back while using the Triplanar (which I see was used in the article you linked, so this problem may not have shown up).
A filter will introduce phase shift, and in a full range system such as yours, will be audible as less bass impact. So its probably best to solve this with elegance rather than brute force.