I am using version 4.2 of BridgePoint but unless anyone has any other ideas I suspect my installation must have become corrupted because it is even worse now. If I create a new project, create a package and create two classes with a single relationship between them I can formalize the relationship, but if I restart before formalizing the relationship I do not get that option after the restart, even though both classes still have identifying attributes. No errors when running the integrity check on the model.
It has been a while since I have done any modeling, but I cannot believe this wasn’t working before. I will try re-installing.