This is exactly what Joe found from high-end A/D, and I found using a Mic2496. If you record the digital signal, you will see the clock moving way too fast, and the playback will be down an octave or so and slow, so you do record 96kH, the machine just thinks it's 16/48. When I imported the signal into Audacity as raw data as stereo 24/96 with a 31 bit offset i could recognize the real me-voice. This sounds much like what the MT II is doing to V3 and other coax digital input, and may be due to a similar bit flag problem. M-Audio is supposed to fix this in new firmware, I don't know what Sony plans to do. Joe did record some analog-in to one D50 at 24/96, and then fed this into another D50, and that worked fine, so whatever flag is missing form the V3/Mic2496/etc. the Sony is outputting it. I seem to recall a similar problem with the Fostex FR-2 or Marantz PMD 671 at high res, they fixed it with a firmware revision. Fostex and M-Audio do firmware upgrades online, the Marantz hads to be sent in to the service center and I fear the Sony may be the same.
Jeff