I have done a lot of work to make the BH DAC as immune to outside influences as I can, but I have not had any time to actually test out how well it really is in that regard.
My guess is that it is not completely immune, that some things will make a difference, but not to nearly the amount as other DACs.
So I wouldn't go about spending time and effort to fix computer "issues" that may not have much affect with this DAC. If you are satisfied with other aspects of the system, I would leave it alone and see what it sounds like first. Once it "hits the streets" I am sure there will be plenty of people doing all kinds of tests with different configurations and figure out just works best and how much of difference different things make to this DAC.
Normally I would say that a good asynchronous USB implementation will beat a good S/PDIF implementation, BUT in this case I have spent a huge amount of effort ( and I really do mean huge) making an exceptional S/PDIF input. The result is that the SQ from all the inputs should be very similar. The upshot is that if you already have an S/PDIF output from whatever, you can keep on using it with the BH DAC and know that you are not loosing anything compared to one of the other inputs.
Currently I have my prototype hooked up USB to a Squeezebox Touch, and an old DVD player over optical S/PDIF, they both sound identical. I can play a CD in the player and I don't hear any difference compared to the USB connection from the Touch playing the ripped tracks. So I think I have pretty much succeeded with this goal.
BTW they both sound amazing.
John S.