What do you mean by manually? Did you do it with an external tool or with a specific method of yours?
About this:
Quote:
I even called session.getTransaction and transaction.commit before session.close and it still doesn't work...
Calling beginTransaction(), then committing at the end is not an option. It's compulsory to correctly demarcate every tx.
About refreshing from the client side, are you sure you don't cache objects by yourself somewhere? In the http session or somewhere else for example?