If the DAC is excellent at jitter rejection then it won't make a difference (one jitter immune input versus another should sound the same as it is all just bits). If the DAC is less than perfect at jitter rejection then it could matter. So your results will vary depending on how well the downstream DAC can handle whatever jitter is being thrown at it.
Does the Transport make a significant difference?
Had been running a squeezebox with my Audio Note 2.1 Dac. Tried my basic Oppo dvd player as a transport and yikes what an improvement - even over my $3,000 invested Modwright Sony player (a little rough round the edges but dynamic and live-ly sounding). So wondering if the mantra of having a great source is the best place to start ... ie matching the Dac to a quality transport say CEC TL 51 or open the vaults and spring for a quality Audio Note, Esoteric, or even dcs transport will be worth the investment. How does this compare with say upgrading your amp or speakers or even cables? I know I should listen for myself but any good experience out there to draw on before I start getting crazy about checking out the used adverts?