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