I would expect that THX can certify the receiver without taking the Audyssey into account because it can be turned OFF. THX won't care as to what processing you do downstream of the signal once it is generated from the player thru the SSP. THX appears to certify the output after the DTS/Dolby logics are applied but not beyond that because the codecs are used to process the original soundtracks in the editing phase and as such are part of the sound.
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Music system
Model 990/7500/Magnepan 1.6 QRs/Technics SL1200 MK2/Aperion S-12 Subwoofer/OWA3/Sony NS75H DVD
APC H15 Power Conditioner

TV System
Large Advent Loudspeakers/ Polk center/Monoprice surrounds/Panasonic Viera 42 inch/Onkyo HT-RC260/Sony BDP S590/Directv


Home Theater System
Onkyo PR-SC886/Outlaw 7125 Klipsch RF-82 L/R,RC-62 center, RB-35 SR/SL, BENQ HT1075, Outlaw LFM1-EX/OPPO BDP-83/Directv
Harmony ONE
Blue Jeans and Monoprice interconnects
APC H15 Power Conditioner