I had the same problem...
Changing the Audio Output Mode from "default" to "Win32 waveOut" fixed it! Go to prefs, audio/Output modules, select Advanced options at the bottom and select waveOut from the dropdown menu.
It's the same problem with AC3filter btw. For some reason DirectX doesn't like SPDIF output, and converts it to standard stereo before sending it to the SPDIF port.
I've already selected Waveout. You understood wrong. I can decode Ac3, DD, DTS. I couldn't decode WMV-HD audio. Because my receiver can not decode that. No way to change that.