how did you upgrade ?
Using eclipse updatesite to update from 3.5 to 3.6 ? That is not (unfortunately) supported by Eclipse since it will most probably cause problems
and since Eclipse it self does not support this JBoss Tools can't either.
If you did it by installing 3.6 and then installing jboss tools and still have problems, then we got a problem and I would still like to see how this "disappearance" looksl like.