@moritz asked me to comment out line set_up_path in /usr/bin/check_mk_agent to test the issue (around line 1930), they’re currently working on it (FEED-6874 in their Jira). I opened an issue through the feedback-2.1-beta@checkmk.com email as I’ve never encountered that issue before on 2.0.
I’m currently waiting for the issue to arise again on all my VMs to see if the one with the modified agent still has the issue or not. It happens about once or twice a week in my case.