It seems there are some steps missing from the build howto when it comes the jakarta-tomcat portion. The original tarball needs to be extracted and everything in the webapps directory needs to be removed. Once that is done, tar the directory.
Code:
tar -xzf apache-tomcat-5.5.15.tar.gz
rm apache-tomcat-5.5.15.tar.gz
rm -rf apache-tomcat-5.5.15/webapps/*
tar -czf apache-tomcat-5.5.15.tar.gz apache-tomcat-5.5.15
Problem solved!