I have succeeded to reproduce the issue.
It happens when installing JBoss Tools 3.3.1 using the Eclipse marketplace client. See https://bugs.eclipse.org/bugs/show_bug.cgi?id=385334.
In this case, Eclipse installs the org.eclipse.mylyn.tasks.ui plugin of the 3.6 version which is not compatible with other mylyn plugins, version 3.8.0.
You can try the following workaround:
- remove (or backup) the org.eclipse.mylyn.* plugins except the org.eclipse.mylyn plugin from the <eclipse_home>/plugins directory
- start Eclipse (Eclipse will start, but some plugins won't be resolved)
- install Mylyn 3.7.1 using the http://archive.eclipse.org/mylyn/drops/3.7.1/v20120425-0100/ update site
- install the Attlassian Connector using the http://update.atlassian.com/atlassian-eclipse-plugin/e3.7 update site
- restart Eclipse (all the plugins will be resolved)
However, it is possible you get an invalid version of the JPT plugin (which is part of WTP). Check the version of the org.eclipse.jpt.common.utility plugin.
If it is 2.0.x, you have the correct configuration. If it is 2.1, you will face the problem described in https://community.jboss.org/message/748871#748871.
If that is the case, the only solution would be to reinstall Eclipse and install JBoss Tools using the following JBoss Tools update site: http://download.jboss.org/jbosstools/updates/stable/indigo/