I ran into the same trouble and found the solution of Denis Golovin is working for me. I selected Hibernate 3.5 in the Edit Launch Configuration Properties window. Aditionally I took hibernate3.jar and hibernate-tools.jar (If you are using reverse configuration control) from plugins to resolve compilation problems on my project. I test it with JPA 2 Type Console. And voila everything workins as ever.
Thanks you all.