OK, thanks for the explanation.
Gosh, it sounds like you have done everything right. Since it is getting to the tones, it is trying to do the measurements. You say the tones are loud, so they should be "heard" by Audssey alright. Be sure the surround speakers are connected to the 'surround' connectors, not 'surround back.' But you have everything else right, so I'm sure that's not it.
By the way, 5.x surround speakers should be to the side of the listener or perhaps just a tiny bit to the side-rear of the listener.
I am at a loss at this point as to suggestions. You might want to call or email Audessey support. This pagehttp://www.audyssey.com/InstallerWeb...eb%2FHome.aspx
has a form to submit question.
One thought, I don't know how it would react if there was an open in the mic connection--wouldn't think it would get to issuing the tones to all the speakers if that was the case, but you might ask Audyssey.