Very strange one here.
When I owned my 350 using my current Denon 2805, the only strange that was a result of the auto setup is that the Denon put the delay (distance) for the 350 around 28ft, even though it was more like 14ft. After reviewing the manual, from JohnK's input, it clearly stated this was normal based on the internal circuitry of some subs.
Your situation seems different, my 350 volume (gain) was usually around 11-12 o'clock to start, crossover turned all the way clockwise (bypass) since I was using the receivers crossover of 80hz. After setup, the receiver levels for the sub was around -2dB. With my EP500 it is at -4dB, with the gain set very low.
I am not familiar with your receiver/amp, so can't help much, but does not seem normal to me. I like Jakeman's steps above, may have to give them a try myself...
