I copied and pasted this from my thread... I bought the Yamaha RX-A2000 and had trouble with my dual Klipsch KW-120's. I felt like you (it was also an upgrade from an older Yamaha model)... didn't understand why my system wasnt working.
Agree with TLS Guy: go down the list and make sure all the settings are setup correctly
* wires connected correctly from reciever to sub
* all speakers set to small w/ 80Hx crossover
* sub 1 set as ON, sub 2 set as off
* the sub level set at 0.0dB (and then try higher levels)
* power amp assign: 7 channel normal configuration
* make sure the AV input is properly set (e.g. AV2 with HDMI vs Optical)
* decoding set up as "straight" (then try other possible settings)
* make make sure the material has LFE info
* try plugging sub back into old reciever to double check the sub
In the end, I just disconnected everything, updated the firmware, plugged everything back in and it worked like a charm... good luck with your system!