I had some audio issues with my RX-A1040. FM Radio,Audio1, and something with something on one of the HDMI's. No sound. After hours of frustration, I found by simply turning the power off and on things started working.
Maybe this will help someone with the above issues.
(LCD - Sony KDL -52 XBR4) (Receiver - Yamaha RX-A1040)(Blu Ray - Oppo BDP-83) (PS3)( Comcast X1) Speakers (L & R - Paradigm Studio 20) (Center -Paradigm CC-470) (Surrounds & Back Surrounds - Paradigm SA-15R in walls) (Subwoofer 1 - Sunfire HRS-12) (Subwoofer 2 - Paradigm PW-2100)