The update made to JULI in Tomcat 5.5.12 brought a new bug: The batch file "catalina.bat" contains the following instruction: -Djava.util.logging.config.file="${catalina.base}\conf\logging.properties" it should be -Djava.util.logging.config.file="%CATALINA_BASE%\conf\logging.properties" instead.
Thanks for pointing this out, I've fixed it in SVN.