SSIS package reading Mysql timeout

I'm a SQL Server DBA that just inherited a MySql database. I have no previous experience with MySql.
I have a SQL Server SSIS package that connects to a MySql database using the .Net MySql Provider. I have the command timeout set to 60 on the SSIS connection. However, the query is timing out after 30 seconds. The Mysql system variables net_read_timeout and net_write_timeout are both set to 90, yet my query times out after 30 seconds.
any ideas what might be causing the timeout?

thanks in advance.