My dev super super had all global privilege boxes checked except for 'File', (using mysql 5.0 and 5.1)
When I tried to remove a database specific privilege for some user this silently failed.
The reason for this is that we try "REVOKE ALL PRIVILEGES ON `test` . * FROM 'piet'@'%';" first and then GRANT all the boxes the were checked.
Since my user did not have the 'File' privilege this was not allowed by mysql. In a comment it states "this query may fail, but this does not matter :o)" but I tend to disagree.
I'm afraid there has to be some code to revoke all privileges that were not selected in the form.