It is a bug in Eclipse. I had exactly the same problem, also on Ubuntu with Eclipse Java EE Juno.
Here is the workaround that worked for me:
{workspace-directory}/.metadata/.plugins/org.eclipse.core.runtime/.settings
delete the following two files:
org.eclipse.wst.server.core.prefs
org.eclipse.jst.server.tomcat.core.prefs
Source: eclipse.org Forum