I was too early to say this is Hibernate issue.
It actually takes quite some magic to make it work,
and there are still some issues with it (see EJB3 timers comment).
Together with Emmanuel we created this test project,
and I actually made it work, but it's very limited in the JEE features.
You have to handle most of the things yourself in order to make it work.
e.g. EM/Session instantiation, Tx, ...
But at least it will shed some light on the subject:
* https://github.com/alesj/hib-in-war/commit/a320e0a2bfe3e9cdf5524ea81da0ef34413ab46f