I wonder why that didn't work for you, I don't understand why it won't just stay on Spdif for you. I checked mine several times today and every time it functioned properly, even if I only used the iFi app for Flac files.
The only other things I could suggest are making sure your DAC is powered on first before powering the ZS on, and not powering it off until after the ZS.
Possibly checking if the behavior is the same using a different Power supply, and coaxial cable, I know silly, but stranger things I have seen, lol
I would definitely report this behavior to iFi support, perhaps they have seen something similar and can advise you further.
Again I will say this is strange, I always remember the ZS default being the Coaxial output, and the USB was "auto-sensing" and did cause some issues long ago, but the coaxial was a constant.
Cheers!!