I'm having the same issue...
I have a need in my applcation to change the timeout value of a transaction programmatically. In order to do that, I had to set the property hibernate.transaction.factory_class to
to org.hibernate.transaction.JTATransactionFactory otherwise calls to session.getTransaction() would throw an exception.
Everything seems to be working perfectly, except that I keep getting a warning:
[AbstractEntityManagerImpl] Cannot join transaction: do not override hibernate.transaction.factory_class
So I'm wondering the same thing. Is it a problem to configure a "factory_class" while also using "seam managed transactions" ?