I have exactly the same problem.
It had already existed when I used the JBossTools predecessor Exadel Studio Pro. Some XML parsing routine seems to have a problem when encountering XML entity references.
Any help in this matter would be greatly appreciated since all my Eclipse projects are marked with a red "x". This makes it hard to distinguish between "real" and "unjustified" errors.
please report in jboss tools jira with steps to reproduce (and keep a reference to this forum posting) - Thanmks.