I am not sure why your system seems to act differently for music vice other audio sources but the equipment should sound the same based on system and equipment response. It could be that the response of the sub is better suited for movies than Music. Or it could be that the room is affecting the sub right around the crossover point such that you hear it more with music. Velodyne used to make the SMS-1 digital subwoofer management. Outlaw sold them for a awhile, but they are no longer. It would give you precise control of the crossover from 15 to 199 hz in 1 hz steps. It also allows you to adjust the slope in 6db increments from 6-48 db. It also analyzes your setup and displays a curve to allow you to make your choices easier.
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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