I recently encountered a situation where an otherwise functioning SCOM agent on a Linux server would not execute shell scripts to run discoveries or monitors. The problem turned out to be an incorrect configuration in
/etc/opt/microsoft/scx/conf/scxrunas.conf, which controls the execution of the following extrinsic methods:
In my situation, the configuration file contained the following, which was preventing the above methods from running with elevated privileges:
Clearing this file and restarting the agent resolved the problem.