First off, I think using the line input on the plate amps is discouraged greatly! I hope when you say that you ran the speakers off of a line out of your IPAD, that you don't mean into the plate amps. Using the speaker terminals, and the line input simultaneously, could have broken the amplifiers.
There seems to be something wrong with the setup however. Any way to test for phase? Maybe one amplifier is set out of phase? Are the drivers moving with music playing?
I will say, that the bass of the E3s is different sounding from any bass I have ever had in my room. Its super tight, but you tend to just hear the intended note, and not the reverberating driver overhang.
It certainly can change the perception of the amount of bass, but it tends to be more accurate to my ears.
Also, I wouldn't discount position. The SS8 and the E3 use two totally different mechanisms for outputting bass, with one using passive radiators, and the other being sealed, front firing, servo. I wouldn't expect them to sound best in similar spots, given how they may differently couple with the room.
How close are you to Jim? Perhaps shipping them back might be in order to make sure everything is working correctly.