I'm having this same problem.
I've been using SPDIF to record into Cubase which has been working fine. The DAW was synced to Virus via SPDIF. Virus audio clock set to Internal, 48 kHz.
Now I want to record the MIDI as well so I connected the USB cable, but it is forcing the Virus to select Sync To Host and switching to 44.1 kHz thus changing the MOTU clock to 44.1 but my project in Cubase was already 48 kHz. I had recorded the audio & MIDI at the last session without a problem, but today I could not get it to work.
Is anyone else getting this?
I am wondering if it is a bug with the 5.0.4.02 Beta OS and if reverting to 5.0.3 would resolve the issue. Or perhaps this behavior is by design.
I am guessing that the Virus is pulling the clock source from the on-board audio sound card and then porting it through the SPDIF back to the MOTU units.
I will try next week to disable the other sound card's driver and see of this resolves the issue.