You might consider this desperation but, it worked for me with an Extigy system.
Dismantle ALL and that means ALL cabling from soundcard to subwoofer to speakers, everything so you end up with speakers and lengths of cable with nothing on the ends of them. Leave it overnight (this doesn't do anything real or scientific but it allows you to recover your composure) then re-assemble everything very carefully. Double check and treble check.
As I say it worked for me. Never knew what it was. Most likely something so simple that otherwise would have been missed.