This is actually the result of a design flaw in the static LogManager. Any class which collects an ILogger in static initialization will only log correctly if the static initialization runs after the LogManager is configured with a LoggerFactory. Any LoggerFactory set on LogManager after that point won't receive any logs.
I am working on a gradual redesign of the logging infrastructure over several commits to work via dependency injection rather than static globals. This will resolve the design flaw and eliminate LogManager altogether.