I was using 20916.1.3 without issue connecting to MySQL & SQL Server databases. When I installed 2016.2 and connected the same way, the schemas do not get populated correctly and I can't connect.
It seems that the UI has changed in 2016.2. If I run 2016.1.3 it works fine. Please go back to the 2016.1.3 in 2016.2. Currently I have to go back and use 2016.1.3 for my development.