I am starting to use MySQL Workbench tool especially for data modeling. So, the first I would like to do is reverse engineering of my existing database on web server. But I
on debian 6, MySQL 5.1.73-1 (Debian), I had the same problem, and a start and stop helped me.
/etc/init.d/mysql stop /etc/init.d/mysql start
not sure what happen, but the problem seems to go away after this quit stop and start, just wanted to add it here, in case others have same problem.