Mikeb:
I wonder if I've experienced something similar a few years back when I tried to sync my symphony orchestra rig (Mac pro, an audio interface and Vienna Symphonic Library) to my Pro Tools HD Accel rig (another Mac Pro) via SPDIF (digital patchbay and a Yamaha 02R96 mixer to Pro Tools 192 IO). Monitoring the audio during the transfer sounded awful. It was totally useless. But I really can't remember if I checked the audio quality of the playback of the tracks afterwards. I just didn't dare to trust the recording quality when the monitoring sounded like that. But then I discovered that the “monitor recording quality” changed when I chose a different master clock. I actually ended up investing in a separate monitor solution after that to avoid similar incidents again. I never found the actual culprit for this weird audio issue though, but now I'm at least careful with how I connect and sync digital units together even if the sync seems fine. I don't know if this info can be of any help to you, but it would be interesting if you could just check your set up using a different way of clocking your audio transfer. Would that be possible? I just got my Kemper a few days back, so I haven't had the chance to explore all the recording options yet. Great product though... 
Cheers,
-terje