This issue may be related to a glitching problem I found in RtAudio, which VCV Rack uses for sending audio to PulseAudio. I was able to fix this issue on my system, and I submitted this fix as a pull request to RtAudio three weeks ago. So far I have not heard back from them.
It is possible to build VCV Rack from source, while including my fix to RtAudio, to eliminate the clicking/popping sounds. That is how I run it on my Linux system. Here are instructions for building Rack with my fix if that is something you want to try.