If you change the name of the workbook, or publish to a different project, there will be 2 copies of the workbook (and thus any sheets or dashboards). If you are looking at all of the "views" in server you will see both dashboards. additionally if you have 2 unrelated workbooks but name a dashboard "Overview" in each work book you will see 2 views called "Overview"
I am using Tableau server 10.1.
Not sure if this is part of what is happening for you.
I am not sure about the custom SQL as I have not used any yet
I completely miss-read that. I thought the duplicates were on the server not in desktop, My above reply is probably worthless. I'm sorry
Can you show a screen shot of your data source tab, before and after the publish