Yes, I'm using qjackctl for changing Jack settings. I can report that after a reboot jack is working again.
I have jack set to use alsa and the idea of using alsamixer was fitting in with what you said about going to the hardware controls. So I have tested alsamixer and yes, it works. The problem is solved! Jack seems to be pretty flaky about settings, though. I tried to change settings to a different mic and it seems to have disabled jack somehow. (Not sure what's going on. I killed the jack process and it won't restart and work. Hopefully logging out or at worse rebooting will fix this.)
I don't think using pulseaudio is the way to control the sound for jack. Pulseaudio and Jack seem to conflict. (There are posts about how to get them to coexist.) Jack has its own settings for which audio devices to use (which was a bit confusing) and it did not pull my pulseaudio settings. And furthermore, pulseaudio is disabled when jack is running. If I play normal sound it actually doesn't play until I quit Jamulus and then pulse audio seems to restart and it plays the normal sound.
I run a weird window manager that doesn't have those panels and normally I control sound using pavucontrol, which is for pulseaudio. But I'm curious because I have both pulseaudio and jack installed and I'm only using jack for Jamulus. Would the sound control panel work no matter what sound service I'm using? Like how does it "know" that I'm using Jack, or want to manipulate the Jack settings instead of the pulseaudio settings?
I installed Jamulus and Jack under Ubuntu 20.10. After finally realizing that I need to adjust the "advanced" settings and specify a sound card I got it working, but my mic level is too high, so I'm going to saturate. Other than sitting 8 feet away from the mic, how can I reduce the mic level in Jack? The qjackctl program doesn't provide any obvious means to do this.