I would try to re-position the sub to another area first and check to make all the speakers are in phase with one another. Next try adjusting your crossover point higher to remove your mains from the equation so they are not adding to your woes. Years ago (and several times since) the woofers in my Advents had deteriorated foam rings and sounded terribly muddy. As you can tell I don't think it is the sub causing the issue, (unless it is damaged) but more of how the sub is interacting with your system and the room. As stated before, I have the predecessor to the X12 but the design is very similar. I get excellent response from it for both music and HT.
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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