Fixed it, turns out the standard logging configuration defines a file logger and also a console logger. The file logger goes to the daily catalina log, and the console logger writes to catalina.out.
Fix was to change in conf/logging.properties:
.handlers = 1catalina.org.apache.juli.FileHandler, java.util.logging.ConsoleHandler
to
.handlers = 1catalina.org.apache.juli.FileHandler
That stops anything getting written to catalina.out