The proiblem with giving advice on motherboard audio is that typically we only know what the controller part is, and not the codec part behind it.
And the codec chip is by far the most important part.
There's nothing wrong with the HDA controller spec. Motherboard HDA audio is potentially just peachy from an SPDIF perspective.
The only system i have with HDA audio is a Shuttle HTPC system that i got for free in return for beta testing some hackneyed video playback software.
In the case of my particular system, the codec is a Realtek ALC882, which will do 16, 20, and 24 bit spdif at 44.1khz, 48khz, 96khz, and 192khz.
And it works a treat, thank you very much.
Mazz's problem sounds like what you get when your codec is upsampling the spdif to 48khz. which is the worst thing it can do.