On my Windows 2000 box. I granted full control of the directory that contains the database to 'Everyone' and that fixed it.
When this happened to me again, this did NOT work. Instead, I had to go through cygwin and set permissions to 777 on the database files, then run the flush command. I'm sure there's a way to do it through Windows, but I don't know what it is.
Although you can also just restart the MySQL service, flush looks like this:
mysqladmin -u Dbradfor -p flush-tables