I found a topic that partially describes my issue, but it is very old, and applies mostly but not fully. I have only the issue that audio is being disabled until I unplug and reconnect the HDMI cable. I've had this issue with all drivers up until and including latest one, Catalyst 12.10.
"HDMI Audio disables when TV goes off"
Windows 7 64-bit
One monitor via DVI
One receiver with dual simultaneous output support (Yahama RX-V767) via HDMI connected to one monitor (HDMI-DVI) and one projector
This Yamaha receiver, when only one output is active (e.g. when projector is powered-off), appear to pass-through the EDID of this one monitor
When output is changed EDID may change without disconnect/reconnect of HDMI between receiver and PC
When both outputs have active units attached (monitor and projector) the receiver sends its own EDID
My two monitors power on at the same time as my PC, and I have no audio issues until I power on the projector, if the PC is running and connected when the projector comes online. Once the projector comes online, "AMD HDMI Output" is disabled saying "Not plugged in". I disconnect and reconnect the HDMI cable on the PC side, and audio is restored. Same procedure (disconnect/reconnect) has to be performed to restore audio after powering off the projector.
I do hope this can be resolved by a driver update in the future.