You write this:
“I just entered a new user, set his permissions to a certain database, set his permissions on some certain tables within this database, flushed privileges after applying to the changes and hit OK.”
I think you did not do exactly what you aimed to do! Selecting in the Object Browser (the left column) has no effect on user management tools. I could figure that that was what you have been doing (only an idea) ??
In SQLyog you define
*GLOBAL privileges in 'add/edit user'
*OBJECT SPECIFIC privileges in 'manage permissions'
Both are in the tools .. user management menu.
It looks to me that you have defined GLOBAL privileges and not OBJECT SPECIFIC privileges. Or you may have defined both! If user shall have no GLOBAL privileges all checkboxes in 'edit user' for this user shall be empty.
What does
Code:
SHOW GRANTS FOR 'user'@'host';
return?
BTW: no need to 'flush pivileges' explicitly yourself when working from the GUI – the program will do!