ERROR - Function 'innodb' already exists
The plugins throwing errors in the error.log were not specifically specified in my.cnf. So I ran...

select * from mysql.plugin


for MySQL 5.6.17 I deleted the following rows in mysql.plugin

innodb ha_innodb.so
federated ha_federated.so
blackhole ha_blackhole.so
archive ha_archive.so


Do not delete anything you are not sure about. The above worked for me as...


I do not use Federated ( accesses data in tables of remote databases )
INNODB is built into 5.6, no plugin required
I do not use Blackhole ( accepts data but throws it away and does not store it )
I do not use Archive ( storing large amounts of data without indexes in a very small footprint )