Upgrading MySQL 5.1 to 5.5 - All tables gone I'm trying to upgrade from MySQL 5.1 to MySQL 5.5.

I followed the instructions here:
http://dev.mysql.com/doc/refman/5.5/en/windows-upgrading.html
I also adjusted the Datadir.

But after the upgrade, all tables are gone. I only use Innodb tables.



The Datadir setting seems to be correct, cause the ibdata1 file changes if I change something in the db. But even if I add a new schema with a new table it does not create a directory for it.
Am I missing something completely?
Turns out I had a mess with the my.ini files. Not sure why ibdata1 still changed, but that was the solution. The mysql workbench configuration was still pointing to the old my.ini file.