Ah, I gotcha... Digital out on the motherboard vs. a dedicated audio card. Not too familiar with the topic (i'm using the far from perfect usb interface), but htpc enthusiasts seem to have asked this frequently. If you assume no resampling occurs, they would both sound the same. However, on board digital outs frequently resample to 48k to comply with the dvd/tv standard.
I guess I'd go with a dedicated sound card that's trusted, like the m-audio!