Tom - your hypothesis is of interest. One observation is that all Thiel speakers mount their XOs to the bottom or back near the bottom with lots of fiberglass between the XO and the drivers / moving air. Plus the sound is hard, like a driver bottoming. When I put the redeveloped XO inside the cabinet, mounted on nylon studs and rubber feet, the problem had vanished. My best guess is some sort of electromagnetic saturation and/or possibly the bottom end of the midrange bottoming out. (But I didn't change the midrange driver, only some specifics of the crossovers.)
As I've mentioned before, getting the XO out of the cabinet does worlds of good. My in-cabinet solution is different from yours - I am suspending each of the 3 small crossover boards in free air, rather than clamping it the the wall where it must absorb the cabinet wall vibration.