You can test for a polarity error with a bassy mono source by trying it with normal wiring and with one speaker reversed. The correct polarity will give a summation rather than a cancellation of the bass.
Floor resonances are usually wide-band since the surface consists of many planks with different characteristics loosely coupled to each other.
I cannot think of how the towel is having an effect unless it is damping higher frequencies that should not be coming out of the woofer.
Kal