When I was using ffdshow audio decoder, I found it was re-encoding all AC3/DTS audio to Dolby Digital 5.1 format 48kHz/640kbps. I know this because my Yamaha receiver indicates the incoming sample and bit rates. So for example, if I was playing an x264 movie that was DTS 48kHz/1536kbps, it would be sent over SPDIF to my receiver as DD5.1 48kHz/640kbps. Similarly, a DD5.1 48kHz/448kbps audio stream would be sent to my receiver over SPDIF as DD5.1 48kHz/640kbps.
I finally figured out that ffdshow audio decoder was the culprit and since replaced it with SPDIFER and my sound quality is also better now (true to the source).
I love ffdshow for video decoding, and use nothing else, but SPDIFER or AC3Filter is the way to go for SPDIF audio output.