It appears I've stumped the masses.
That's okay because the problem mysteriously disappeared.
Even in working with Mentor we never identified the issue.
What I believe is related is that the update libraries function when updating against our Oracle database adds duplicate properties into tables.
For example I have a field Case_Code, update -properties added 3 duplicate case code fields to one table, doesn't happen in MS Access.
For those of you who may have read this and are curious, it appears it's a timing issue with the ODBC driver and the SQL query.
We had issues where tables wouldn't appear, "0" was populated in empty numeric fields, and then the issue with duplicate line entries in the database configuration.
We use Oracle for our database which has thousands of tables and releationships, we wouldn't use MS Access for a globally served database.
What we found was this:
Disabling the timeout setting in the ODBC driver fixed the missing tables.
Creating a longer query timeout in the databook seems t have fixed the duplicate line items in databook.
The "0" populated in undefined numeric fields went away on it's own. .again possibly still a timing issue.