I'm not surprised different inputs sound a little different. First see this reference:
http://dagogo.com/benchmark-media-dac1-review-part-1 referring to John Watkinson's article in Resolution titled "The Cable Snake"
Another excellent reference are the white papers at the Grimm Audio Website, where they have the high resolution measurement tools to measure slight improvements in low frequency jitter performance even when feeding into a phase locked loop, from a "more perfect" digital clock source. These people know what they are talking about and can buttress their claims with facts, not fancy.
That's the technical side of the argument in favor of the placebo effect being the dominant factor here.
However, despite all this above placebo-likely situation, it appears to be true that despite many DAC makers' claims of "complete" jitter immunity, there is a small residual possibility of audible jitter due to different input topologies or cable differences being audible, due to the DAC's inability to reject all of the incoming jitter. HOWEVER, this residual with a well-designed DAC is usually so low that it takes a real expert to reliably hear the difference on a very high resolution playback system and even then there is room for doubt. These kinds of audible differences are so subtle that it is not the kind of thing that sounds "obvious". Especially if you do successive playbacks after minutes of silence, a sure recipe for the placebo effect.
Bottom line: if you start worrying about your DAC performing or sounding different with different inputs, then get a life and get a job! Or get a better DAC! There are more important things to worry about, the differences assuredly (with a well-designed DAC) are at the threshold of audibility and inconsequential even to the most critical audiophile's listening system, in my not-so-humble-expert-opinion.
JItter is audible, though, and I urge those of you wishing to train your ears to hear it. Visit
http://www.cranesong.com/ and click on the link to learn what jitter sounds like. David Hill of Cranesong has induced various types of jitter into a file and made it obvious for ear education. Take advantage of this education so you can be sure that you know what you are talking about and what the real sonic symptoms of jitter are.
Best wishes,
Bob
I have a Ross Martin Audio Super Beast DAC that accepts two optical digital inputs, two coax digital inputs, adaptive USB, and AES. It has a switch that lets you immediate change which input is being used.
I decided to try connecting several inputs and switching them to see ...