Upgraded from 5.1 to 5.5 but old databases do not appear

[Chris Sarris]

Hello,
I am running on Windows Server 2008

I just upgraded my working MySql 5.1 install to 5.5 using all of the MySql official documentation. When I got done - 5.5 started but my existing databases are not showing up via a "show database;" nor in phpMyAdmin.

Nothing in the official documenation http://dev.mysql.com/doc/refman/5.5/en/upgrading-from-previous-series.html
talked about moving my data or how to migrate the Permissions/Grant Tables.

I am left with a broken production environment for 100s of students.

I have searched Google for "No databases after MySql 5.1 to 5.5 upgrade" but have not come up with a conclusive answer.

I could copy my "data" folder from the 5.1 to the 5.5 install - but I am concerned about copying the "mysql" database over - as it is holding all the perms.

I know I need to do a "mysql upgrade" after all this.

I would appreciate some solid direction to a Windows person.
tks.