JIRA Standalone logging broken

JIRA 3.3 now comes with Tomcat 5.5, and the switch seems to have broken logging quite badly:

• Plain stdout / stderr logs are completely lost.
• Editing the log levels in the admin section does not work properly. It looks like the log levels apply to Tomcat as a whole, not just to JIRA:
• Increasing the root category level to DEBUG causes Tomcat internal logging to print (JspServlet, etc)
• If I increase the verbosity of a named package (eg. AccessLogFilter), the new logs appear in atlassian-jira.log, but not in catalina.out. Nothing appears there until I also increase the verbosity of the default (root) category.