So in addition to the databaseOwner setting, what about the objectQualifier setting also in that same area in the web.config. Any difference from the old and new files?

Nope, if it is empty in both instances you should be fine. That setting makes the DNN tables prepend information onto the front of their names

For example, without objectQualifier the USERS table is simply USERS

WIth an objectQualifier="dnn" the table would be called DNN_USERS

That can also cause the problem you see, about not being able to find the objects in the database.