Also, you don’t want to be using alsa_in. It resamples and adds significant processing load leading to higher risk of xrun.
48000 samples per second is not the problem. I can run soundcards at that rate. How do you know there are no xruns? Clicks every second sounds like a clocking issue with xruns or maybe a mis-match of buffers. (I just spent too much time tracking down an issue where an application seemed to required a specific buffer size in Windows 10 but not in Windows 7.Stoopid Windows!!!)
Do you have an option within the Ui24 to define its audio clock source? It may be running from a different clock to the Zynthian. If there is an option to use USB clock then try that.
I assume you are using the Ui24’s DAW USB to connect to Zynthian. (It has lots of USB which each behave differently.)