OMG - what is going on with Eclipse (3.3 Europa) - has anyone come accross this problem (bearing in mind I have been messing about with uninstalling different Tomat containe
Probably the easiest way to get past this is to define a new server.
Right-click in the Servers window and select New, or when you do 'Run On Server' select Manually define a new server. You can have multiple servers defined using the same Tomcat runtime (they'll all have separate configs and deployment directories defined by -Dcatalina.base=...), but don't run them at the same time unless you change the ports they're listening on.
The new server will use a path like
<>\.metadata\.plugins\org.eclipse.wst.server.core\tmp1
for the Tomcat conf and webapps directory.
Try running on this server. If it works, you can compare settings with the old one, maybe try deleting the app from it and re-deploying, and figure out what you might have done to cause the problem. Or just delete the original server config.
As far as your second problem, I'm not sure. I'd try a new server config first, get it working, stop the server, do a 'Clean' on your project, delete anything in the tmp1\work\Catalina directory, and restart the server (you could remove and add your project to the server again too to be really clean).
Check the console messages too to make sure there were no errors related to this.