@OP You indicate that there is no rumble when the Aexthetix phono stage is played via your Apogee. It's not impossible that the sub is reproducing frequencies that are below the bandwidth of the Apogees.
In terms of fault finding, you should borrow an alternative phono stage from your dealer - preferably solid state.
If that eliminates the problem then you know that the issue is interaction between the turntable/sub/phono stage.
Tubes are microphonic and the IO is relatively unusual in using tubes for all of its gain so the issue is, pardon the pun, amplified.