I am having exactly the same problem! I am connecting using an ODBC connection. The ODBC connection is using PuTTY to connecti via an SSH tunnel to a MySQL database. My queries execute correcty in my usual software, but, I cannot get Qlik Sense to work.
On some of the older versions of Qlik the AD authentication didn't work for me so I had to use a service account. Might try hard coding your connection (username / password). AD authentication seems to work fine on Feb 2018.