See discussion at https://gerrit.wikimedia.org/r/171618
Briefly: We're using the default logger (which dumps to stderr) instead of the bunyan logger (which is configured in localsettings.js I believe).
I think what's happening is that we don't actually read localsettings.js at all in the master thread.
So timeouts and other messages reported by the master thread don't make it to logstash.
Version: unspecified
Severity: normal