In addition to John's usual good advice, I would suggest trying the system with Audyssey turned off, especially if the 3808 is an early model and not updated, I never liked mine until the last update, although I am quite sure the last update didn't fundamentally change Audyssey. You may find that the EQ in Audyysey has sucked all the bass out of it. You may also want to try the LFE setting at LFE+Mains.
If this problem is just in 2 channel, there is a seperate setup screen for 2 channel listening and the sub has to be turned on in this setting.
I am wondering, was the volume(gain) on the sub set high during the initail setup? If so turn it down and then rerun Audyssey and leave the sub level in the 3808 at 0, once the program is done(do at least 2 positions for the setup), You can then increase the sublevel in the receiver as desired again.
DO you have an SPL meter? If so, try setting the speaker and sub level manually, If you are unable to get the sub to the same levels as the mains with pink noise from the receiver, there could be a problem with the sub.
