When I got in to the office we reproduced a facsimile of the issues reported here on my Mac Mini. What we did was take a DAC that had been running properly on all sample rates for an hour or two on USB. I powered it down and disconnected the USB cable. Then I switched the selector to SPDIF. Then I powered it back up and plugged in the USB cable. The Mini was left on, with Amarra running (not playing music, just open) the whole time.
With the DAC still switched to SPDIF, the DAC display read 44.1. When I switched it to USB it read 352k. Audio MIDI settings on the Mac showed 384k. Playing any 48K multiple sample rate would only run at a multiple of 44.1K - i.e., 96K ran at 88.2k, 192K at 176K, 48K at 44.1K, etc.
Solution:
So I unplugged the USB cable from the DAC, powered it down.
Shut down the Mac.
Made sure DAC was set to USB.
Connected USB cable to DAC.
Powered DAC up.
Booted up Mac.
DAC shows 384K, or whatever the last Audio MIDI setting was, and functions properly.
Please try this exact undo/redo sequence and let us know if it resolves the issue. I'm afraid I don't have a Linux box here, but I'm sure John is working to reproduce the issue on a Linux box.