I'm seeing this issue as well. On my Hopper connected to my AVR it always boots in 2.0 until changing channels.
On my Joey, connected to a Panasonic TV, it will boot with no audio at all. To get audio back, I have to either re-connect the HDMI cable, or change to a channel that is 2.0 (usually an SD channel), then change back to a 5.1 channel. I have a powered HDMI splitter in-line for the Joey (the other TV has no issues), and I've always kind of assumed the audio issue was related to the splitter and not the Joey, but the Hopper is a direct connection to the AVR.