We (I, working with support) tried pretty much every variation of installing/uninstalling Firefox, Flash 32bit, Flash 64bit, Flash from within Firefox, Flash standalone, etc etc. I finally gave up, especially once I read that Boxee was ending development of the Windows app anyhow.

Might I suggest checking out XBMC or Plex? They don't do the nice integration of all sources and sharing, but they do work for all the same media sources Boxee supported (I went with XBMC myself, especially with the new Eden release - very nice product).