USB: that's a shame. Maybe an external powered USB hub would solve the problem?
It could be any number of things, judging by a quick search - so far I've seen solutions involving ASIO drivers, USB ports, even length of USB cable - but at least you now know that the speakers are fine.
And I'm relieved, after all that hassle, that you like the D5s as much as I do
Regarding settings, it's mainly a case of trial and error, depending on what sounds best. But I'd start with the boundary: 2 for the one with the back to the wall; 1 for the one in the corner.
If they sound noticeably different [not just louder, but tonally different] then you can probably bump the corner from 1 to 2 [the boundary setting is just a bass-trap compensation roll-off, from what I can gather].
Next, play some music that you know the stereo positioning of [e.g. one where vocals are right in the middle - they usually are - and has instruments that pans from one side to the other [e.g. a roll on the toms]. Adjust the sensitivity of one speaker until the sonic balance sounds right, and those vocals are dead centre. It's unlikely they'll both have the same sensitivity setting due to your speaker placement and seating position, but tweak until deliriously happy
edit: Which media player is best? That's a whole new thread. Go create it, and watch the fur fly
SPDIF from computer: Yes, that's probably right - it depends on whether your soundcard passes through digital [*good*], or whether it does a digi > analogue > digi double conversion [*not so good*] Reconversion seems unlikely, but I don't know much about modern sound card architecture].