Athena Query times out after upgrade to Version 3

Some of our queries time out after we upgraded to Version 3. The query with the id below takes around 3 minutes on Version 2, and sometimes times out and sometimes returns in 45 minutes in Version 3.

What do we need to do to make it run as fast as in Version 2?

Error: Query timeout This query ran against the "production" database, unless qualified by the query. Please post the error message on our forum or contact customer support with Query Id: adc17b60-a55c-475a-ad75-b0af413492b4