Some logs don't go to atlassian-jira.log log file

JIRA 3.2 JIRA's log4j configuration is set to log to a 'atlassian-jira.log' file in the directory JIRA is started up from (this is to get some logs from Windows console users, who otherwise have to cut & paste). However due to an oversight, only logs from 'log4j.rootLogger' get sent here, not logs from categories overridden further in the file.