With the 990 set to "large" for the front speakers, no signal should be going to your sub. Since all of the bass is coming from the V-2s, you might want to experiment with their placement. Have you tried setting the 990 to "Small" with a Xover of 60 or 80hz. That would take the V-2s out of the picture at least temporarily so you could compare the effects. Make sure your bass and treble controls a set to neutral so you are not artificially boosting the bass.
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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