hi Henk,
Could you open https://jira.jboss.org/jira/browse/JBIDE describing the setup ?
I can tell you that OpenShift, eGit and GAE should not affect any of this since those we use/test with already.
Could you try adding each of Glassfish, weblogic and mercurial plugins and retry the start/stop of EAP 6 and let us know when it stops working for you ?
(A more likely explanation is though that you have an older JBoss Tools version installed which is not compatible with EAP 6/JBoss 7.1.2 shutdown which we did have to fix in the JBoss Tools 3.3.x beta's)