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Documents duplicated after upgrade to 6.1.1/6.1.2

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Holidays are over so I am finally trying to upgrade my site to the newest version (I know it is now 6.1.2 but that does not resolve the problem) and I'm having about a hundred issues. I have found answers to most of them here but have not found this one yet. I am getting the stock CC install database data like a fresh install but this is an existing site and database.

After I upgrade and then manually update the global.inc.php file to bring the store admin back up and working I am seeing that the database has errors. It seems that it is writing the default data to the tables as well as leaving the data that is already there. I have only done this on a few test sites so far and the store setup settings are stock out the box Cubecart so I'm not sure if this is overwriting that info too.

I am not seeing the normal options for the database for upgrade or to overwrite any existing tables when I upgrade automatically. That seems to be the issue. Is this an issue anyone else is having? Anyway to avoid this before I upgrade my main store?

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