Could you elaborate on that? I don't recall any EQ issues with the X-Fi Prelude over S/PDIF, though I hooked up my SU-DH1 to it less often than my X-Fi Titanium HD. I'm willing to run some tests to confirm or deny these issues, though.
Also, with X-Fi cards, the "Speakers" device needs to be the default audio device in the Windows sound control panel, NOT "SPDIF Out". You just check a "Play Stereo Mix using Digital Output" box to get it to output through S/PDIF. Weird, I know, but it's the only way I've managed to get any sound out of the S/PDIF output for things other than DVD movies.
I'm not sure how it works out on other sound cards (different driver control panels and all that), but it's something to keep in mind.