I undergo what seems like a bug on a quite random but frequent basis.
It happens sometimes that I create an Entity (which by default is called UnnamedEntity), which I rename to the name I want (for example MyAwesomeEntity). Even if the Entity Block appears with the correct name on the diagram and the entity list, it still appears with "UnnamedEntity" on the fields for a association or a many to many relation.
And when I export to my ORM (Doctrine 2), the class name is "UnnamedEntity", and so is the Namespace (....\MyBundle\Entity\UnnammedEntity).
I would like to help you reproduce it, but I can't do it. It really happens randomly, I don't know how.