Try using the longer cable as the input to the first sub. That will tell you if the long run is bad. Then connect the shorter cable to the back sub. That will tell you if the sub has a problem. You will have to move the back sub to the front but it will make it clear what the problem is. I have two subs which I have connected to my Onkyo 886 via a splitter and the cables are different lengths but they work perfectly. I'd put my $$$ on the daisy chaining vice a bad cable. On another note while you are getting a splitter, get two 90 degree couplings for your subs and reduce the stress on the connections.
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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