...Right... but that's not the issue... I, for one, don't use any AC3 passthrough-able media in MythTV... I would expect that I would have stereo sound if that box isn't checked - I have no sound at all.
The issue is that I can't have normal stereo audio working in MythTV at the same time as I have AC3 passthrough for DVD/video playback.
I'm interested in what changes between the "Manual configuration" setting and the others where you can check "AC3 passthrough" on the Wizard --> Devices --> Media Directors page.
I'll look out for a way to incorporate the MythTV AC3 passthrough setting though.