KMILLER5-I recently answered a very similar question via A-B audition, as follows:
All Audio Research Equipment with true balanced circuitry--AR DAC 2, AR Pre-Amp, AR Amp. Kept a Transparent Reference MM running from the Amp to the Speakers, and Transparent XLR, Balanced cable running from the AR Pre-Amp to AR Amp throughout the testing.
A-B tested the cable running from the AR DAC 2 to the Pre-Amp with SE Transparent Reference vs. XLR Transparent Ultra. There was a difference.
One man's findings: clearly more clean volume with the XLR Ultra--perhaps a tad "tunnel like" but nothing that jumps out at you unless you're comparing it to Transparent Reference.
With the SE Reference, there was more detail and a wider range of detail. For instance, Diana Krall's voice sounded great with the XLR Ultra, but that slight lip smack she does at times, just sounded more "present" with the SE Reference--you knew she was just a feather's width away from the mike with the SE Reference.
Guess: Transparent says the difference between the Ultra and the Reference and the Reference and the Reference XL is a matter of build quality tolerances. I'm just guessing, but I'd say it was also a matter of design. Somehow the Reference shunts away the grit and grime of stereo electronics more precisely than the Ultra. Not that the Ultra is in anyway worse sounding, but in a way that the Reference is better sounding. I know, sounds crazy.
A final guesstimate: there may be something going on along the line of synergies within model lines, ie. all ultra interconnects vs. all reference interconnects.
Hope it's not too late, but if you've decided already, let us know what you found... WM2001