Did you set up the default Business Unit ? Did you setup your Global/User Options? Are there any errors? Do you have a screenshot?
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Also working on this issue, we found the updates were not being pushed to the database. This was because the server running FSUpdate did not have bcp.exe (Bulk Copy Program) on it. This is part of the SQL client tools. Installed SQL Native client and then the SQL command-line tools and it now has updated the database with the packages. http://www.microsoft.com/en-us/download/details.aspx?id=16177