As Michael indicated, it is generally an accepted practise to ignore this aspect of the J2EE spec (for example, jboss usese log4j and regularly writes flat log files...)
An application server (like JBoss) may use files or anything else it needs. The spec is about the applications running inside the application server.
Nevertheless, the problem is not the usage of files, the problem is the synchronization which is done by log4j independent of the appender.
Every call to a logger and most of the calls to an appender (derived from AppenderSkeleton) are synchronized.
If you use the FileAppender anyway, don't write to the same file from different nodes in a clustered environment.
Ingo.
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