OK. I was having the same issue. Here is what I did to temporarily resolve it. After getting the system up, to where the mythtv is playing via digital audio, open the webadmin, go to the media directors page, and on the media director you are using digital on, from the drop down box under audio, select stereo. But leave the AC3 box checked. At the bottom click update, and then do a router reload. Now my videos and my mythtv play using the digital output.
This is not a fix, and there is an issue, but it can be used as a temporary workaround.
Hope this helps.