Hi
I have had the same issue over recent weeks, I'm afraid I don't know how to fix it BUT I do know how to work around it.
All you need to do is setup ODBC connection(s) to your MySQL database(s) and then chose the ODBC connection method from Power BI "Get Data" menu.
You'll be able to select the ODBC database from there and choose the tables you need or if you select the Advanced option you can commit a SQL statement as you would do if the MySQL connection option was working.
A side point, I have this issue with 2 of the 3 MySQL servers I use, 1 of them however works absolutely fine through the connection so I can only imagine the issue is server side....but that's about as far as my technical capabilities extend 
Hope that helps
Mike