I had the issue from the original description.
I was able to stop it manually using 'mysqladmin shutdown -u root -p ...' Then followed the instructions here:
http://mirzmaster.wordpress.com/2009/01/16/mysql-access-denied-for-user-debian-sys-maintlocalhost/
And after starting it again I was able to stop it successfully. Then I retried the upgrade from Update Manager and it worked. Up and running on 5.1.37.
I had the issue from the original description.
I was able to stop it manually using 'mysqladmin shutdown -u root -p ...' Then followed the instructions here:
http:// mirzmaster. wordpress. com/2009/ 01/16/mysql- access- denied- for-user- debian- sys-maintlocalh ost/
And after starting it again I was able to stop it successfully. Then I retried the upgrade from Update Manager and it worked. Up and running on 5.1.37.