Since this thread is the only one close to my problem, I´ll just jump in here.
I currently have a similar problem as described in the initial post.
When running mycroft in debug mode it starts up perfectly normal and recognizes voice commands (apart from the fact that no skills are loaded yet). After a minute or so the microphone level display just freezes and it wont recognize any commands anymore. When restarting mycroft the same thing happens again, mic is working for half a minute and goes dead afterwards.
One thing that seems even stranger to me is the fact, that after a few minutes running mycroft my pi just freeze completely.
I have a Raspberry Pi model 3, running the latest version of raspbian stretch. I installed mycroft with the git clone method and have earplugs as audio out and a usb mic as input.
I searched all mycroft log files for error messages, but to me they seem like mycroft is working fine. I already tried reinstalling mycroft and reflashing raspbian however the bug is still present. Another thing to note is that the error occurs on both the current master and dev branch.