I migrated Eclipse 3.2 to 3.3.1, at first I used the same workspace and I had some problems with myln plugins and the server did not start correctly. Then i tried with a new workspace and everything was smooth except at server startup:

Timeout waiting for Tomcat v5.5 Server at localhost to start. Server did not start after 45s.

You need to set server timeout delay = Unlimited from Window>Preferences>Server…