Welllll, after a friendly chat with the ffdshow folks, our problem is a feature not a bug. ;-)
They tell me that the AC3 is in a S/PDIF wrapper and the files plays back fine if you use AC3Filter. Just not with ffdshow(?)
They did ask me to see if I could figure at what version the change was made, so they MAY fix the problem (unless for some reason it is necessary for people that actually use that feature for what it was intended).
Anyway, on the bright side there is a work around for the newest builds that involves an extra filter and the extra step of creating a 5.1 (or however many channel) wave file and then using your favorite DD encoder on it.
On the up side, it gives MAJOR flexibility to the guide to allow for more modern forms of DD, DTS and/or lossless tracks. (Which I suppose I could have included in the guide earlier).
I can't see asking people to install a 2009 build of ffdshow just for upmixing, so I'll give the ffdshow devs a chance to fix things. If that doesn't pan out this guide will get overhauled. (Probably with screenshots.)
@dark_jedi - I think jdobbs' reason might be that Beta7 is the most recent 'official' stable build of ffdshow. The rest are test builds.
Yeah, it's been quite a while since the last official release.