Chris:
IMHO, the only way to validly conduct this test is to a) not be working with dithered/resampled test tracks; and b) have test tracks that are, in fact bit-perfect identical to one another. This means that not only would the md5 need to pass on each track when going between the 722 and the destination device, but that each track would need to have the exact same md5 signature (this means that each track is bit-identical to the other). This is what Brian was able to accomplish in his testing example above (i.e. the source>spdif>destination sample was bit-identical to the source>firewire>destination sample).
If you think about it, each sample that's recorded is nothing more than a series of numbers. If either the spdif or firewire transfer is changing the way the numbers are recorded on the destination device (computer) then you're not achieving a bit-perfect transfer and the device that's changing the zeros and ones is the cause of the different sound you're hearing. It's my belief that one bit-perfect transfer should ultimately sound exactly the same no matter what the means of transmission or recording (i.e. bit-accurate transmission of the digital data via morse code or smoke signals should sound no different than bit-accurate transmission via firewire, spdif, ethernet, usb, etc.).
I can fathom how the use of clean ac power, better/less jittery cables, etc. can make a difference in the way an analog signal sounds or in the effectiveness of an asynchronous digital transfer, but simply can't see how otherwise bit-identical transfers can sound different throught the use of different transfer means.