Sound problems are the bane of Boxee on Linux. I had similar issues when running the Alpha (I posted my attempted solutions at the time), and thought they had gone away when I first installed the Beta. However, when I got the Beta up and running on a new HTPC - no sound. I came across the following:
I only had to work through to Step 4 and the sound was back. The article is the clearest explanation of Linux sound I have read and it's the one I will turn to from now on.
Boxee Beta on Dell Optiplex 745 (Core 2 Duo) running Windows XP
Boxee Beta on HTPC (AM3 Dual Core) running Ubuntu 9.10