While on Tomcat 6 and Eclipse Ganymede I found out the following chain to work like charm:
1 stop server
2 project -> clean
3 project build (I had automatic build disabled)
4 delete server
5 delete Servers folder
6 restart Eclipse
7 create new server, add project and start 🙂
takes some time but worked like charm. My problem was a irritating Listener start problem, but this seems to be something similar: a property at tomcat. Btw: nowadays I am also a big Glassfish fan.