I have the same issue, but my setup is a bit different.
Upgrading from a Mini Converter Audio to SDI that's been working for years with the Teranex Mini (to clean up the rack install). 1080i59.94 from switcher embedding 48k AES/EBU from a TC Electronic Finalizer 96k.
With the Terenex, there are consistent audio artifacts that sound like clock drift or something. Sounds exactly like the audio linked above. Verified all switches and tried with sample rate conversion enabled and disabled (no change).
I went back to the old Mini Converter and everything sounds how it should.
I think there is an issue with these and would like to know if you ever found a solution