I was able to track the problem down to the older UR22 models supporting a minimum buffer size of 512. JackTrip uses a default of 128, and from versions 1.8-1.10 was not doing a good job adjusting when the configured buffer size isn’t supported by the audio interface. It’s likely that other audio interfaces and drivers with the same limitations had similar problems.
This is now fixed in JackTrip 2.0.