I reported on the avsforum thread that I couldn't get passthrough to work, but I've since found that I can get it to work sometimes. I'm testing with GraphEdit because the behavior is intermittent with Zoom Player (WMV Pro v.4.00 beta pre RC1) and Media Player Classic (6.4.8.1).
From my observations in GraphEdit, I think the setting "Main > Options > SPDIF" is not being loaded when AC3Filter initially starts.
If I launch GraphEdit with the SPDIF option already enabled and create a graph with AC3Filter decoding an AC3 stream, GraphEdit will not perform as expected: nothing happens if you click play, and if you click stop GraphEdit will hang for 10 seconds and give this error message: "The graph was unable to complete pause within 10 seconds. Press Retry to wait another 10 seconds for completion or Cancel to attempt to stop the graph". This will happen regardless of what "System > SPDIF passthrough > AC3" is set to.
However, if then I access AC3Filter properties (from within GraphEdit, not the Start menu), disable and re-enable the SPDIF option, then press play, the graph will play as expected: passthrough will work fine if it is enabled; if passthrough is disabled, AC3 Encode will work but drops out after an undetermined amount of time, even with low (<10%) CPU usage.
Also, if I load GraphEdit with the SPDIF option disabled, then enable it after starting GraphEdit, it will function as expected.
This strategy does not seem to work in Zoom Player at all, and it works a little bit in Media Player Classic (I've done very little testing with either, though).
I've tried this with a variety of sources (vob, ac3, mkv+ac3, avi+ac3) and filters (various splitters) and the behavior seems consistent, so other filters don't seem to have an effect on this.
Some info on my PC:
Win2K SP4, 2.2GHz AMD Barton, nforce2 motherboard (note: AC3 encoding is disabled in soundstorm), 512MB RAM.