IModelDocExtension::GetObjectByPersistReference3 Problem, Please Help!

I am using GetPersistReference3 Method (IModelDocExtension) In an application that does the following.

visits all configurations, all features, all display dimension.

I am having an issue where the persistent reference does not persist. I have narrowed it down to SaveAS. and also might have something to do with derived configurations.

I have one part with default configurations, and 2 derived configurations. where one of the two derived configurations has its own incremented persistent reference.

Anybody have a clue?