JBDS 3.0.0.GA includes JBossTools 3.1.0.GA.
You probably faced https://bugs.eclipse.org/bugs/show_bug.cgi?id=299808 and duplicates which is related to concurrent access to EMF model from different threads without proper synchronization.
Eclipse issue is fixed in HEAD and should be available as part of WTP 3.2 which is for Eclipse 3.6. The only way you could get fix for it is switching to eclipse 3.6, WebTools 3.2 and JBoss Tools 3.2 nightly build. Last version is available from download site here http://download.jboss.org/jbosstools/builds/nightly/trunk or from update site http://download.jboss.org/jbosstools/updates/nightly/trunk.
It might be also unstable because it was migrated to eclipse 3.6 only couple weeks ago and still gets many changes every day.