That is most likely because you created a many-to-one association. In that case, all objects point to the same object steering the check-box.
Can you change it so many object from the Entity containing the boolean Attibute can be associated to many objects from the different table? This can be done by creating a many-to-many association. It could also be that you have an error in the Domain model (from a functional perspective.
Paste a screen-shot of your Entity model and explain the reasoning why the association is like it is now. After that I can tell you what you need to do.
Go Make It