We encountered the same problem.
Go to the \JBoss-2.4.4_Tomcat-4.0.1\catalina\work\localhost (or whatever your hostname is) directory can delete the files under the directory with the same name as your webapp. Or delete the whole directory with the same name as the webapp.
We ended up creating an ant task to do this as part of the build and deploy process.
The problem is a bug in Sun's file: protocol handler.
It reports all files as last modfied in 1 Jan 1970.
This has been fixed in java 1.4
JBoss3 has recently added its own file: protocol handler
so this problem should go away with java 1.3 as well.