I think I got the identical situation under an earlier Tomcat - maybe even a 3.x one. I'm not yet able to run Tomcat 4.1 because my
EJB server currently only work up to 4.06, so it's not exclusively an Tomcat 4.1 problem.
Unfortunately, I don't remember how I fixed it. You MIGHT be able fix it by manually purging any previous unpacked WAR (delete the unpacked directories in $TOMCAT_HOME/webapps AND in "$TOMCAT_HOME/work/localhost/".
If that doesn't make it happy, what I'd do is ZIP/tar the existing tomcat directory in its entirety and remove the original (e.g. "-m" option on ZIP) so that you can retrieve config files as needed, then re-install Tomcat4 from scratch.
Wish I could be more specific, but I DO know that Tomcat doesn't bother to purge certain things that it would be safer if it did, such as stale webapp files.
Good luck!
Tim
The secret of how to be miserable is to constantly expect things are going to happen the way that they are "supposed" to happen.
You can have faith, which carries the understanding that you may be disappointed. Then there's being a willfully-blind idiot, which virtually guarantees it.