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I have just today tried to use the "Create new connection" in the load editor of Qlik Sense Desktop February 2018 Patch 1 (12.5.3) to make a new connection to my local Microsoft SQL Server 2016.
If I do it with OLE DB or with ODBC it all works very well. I have tried any of the different ways of specifying my local instance as server in this dialog nothing seems to work:
I get either this:
Or this - depending on whether I put OX790, . or (local) into the servername:
did you tried to connect to your database with the original Microsoft Driver?