To expand on the above I've been doing a bit more testing on this today. For reference running Vista SP1, playback through media centre using an ATI4650. Haali and ffdshow are installed and both working 100% outside of media centre for spdif passthrough, tested in zoom player and WMP11.
However inside media centre spdif passthrough refuses to work for either AC3 or DTS. Amp indicates it's getting on signal and haali is not showing any audio stream (video is fine). Changing ffdshow settings to allow it to decode the audio and pass PCM to the AMP works fine.
One final oddity is that if I right click a file in explorer and select open with media centre, then it opens and plays fine bitstreaming the AC3 or DTS to the amp and letting it decode! This makes no sense to me whatsoever, and all I can conclude is that media centre running initally somehow blocks spdif passthrough, whereas opening it by running a file doesn't have this block kicking in.
Does anyone know how/why files are handled differently in this situation, and more importantly any way to fix it?