Are you sure that the LFE output has not got turned down, below the sensitivity of the subs auto on circuit. Go into the speaker menu, and turn up the juice from your LFE output and see what happens.
Do you have a disc with test tones, and an amplified meter? If you do play a low frequency tone at high level and measure the output at the LFE terminal. You should get at least 2 volts AC. If you don't and the sub is turned on and the output is turned up on the receiver, then something is wrong in your receiver.
We get a number of puzzlers. I'm starting to think that every dedicated HT owner should have a a minimum, a high impedance amplified meter, an oscillator and a two channel scope as a minimum, and of course learn how to use them.