That is exactly what I was thinking.Default will be set as InnoDB for MySQL 5.6. AFAIK the same was true for MySQL 5.1. However, that doesn't mean that the tables themselves will be in InnoDB format. Before MP 1.6, we explicitly set the table format to MyISAM.Following the steps at http://wiki.team-mediaportal.com/1_..._Tool)/Update_to_MySQL_5.6#Useful_information, I do have InnoDB.I'm curious. Are your database tables now in InnoDB format? I would bet they are still all MyISAM.
You installed MySQL 5.6 but configured the database connection with MP1.5. So, in this case MP creates 'mptvdb' with MyISAM format.
After that you updated MP to 1.6. The installer found an existing database and left it unchanged. That means, that your tables remain in the same format as before.
To overcome this situation you have to delete the 'mptvdb' database (use the Workbench) and configure the TV-Server database connection again. In your tutorial these are the steps 6-9. After that MP1.6 will create a new database with the new InnoDB format.
To check the format you can use this sql command (also in the Workbench, when you have connected to your database):
SELECT `TABLE_NAME`, `ENGINE` FROM `information_schema`.`TABLES` WHERE `TABLE_SCHEMA` = 'mptvdb';