You say you've had problems with Navicat. For the record, I use Navicat and I haven't experienced the issue you describe. You might want to dig around, see if there's a reason for your problem and/or a solution, because given the question asked, my first recommendation would have been Navicat.
But if you want alternative suggestions, here are a few that I know of and have used:
MySQL has its own tool which you can download for free, called MySQL Workbench. Download it from here: http://wb.mysql.com/. My experience is that it's powerful, but I didn't really like the UI. But that's just my personal taste.
Another free program you might want to try is HeidiSQL. It's more similar to Navicat than MySQL Workbench. A colleague of mine loves it.
(interesting to note, by the way, that MariaDB (the forked version of MySQL) is currently shipped with HeidiSQL as its GUI tool)
Finally, if you're running a web server on your machine, there's always the option of a browser-based tool like PHPMyAdmin. It's actually a surprisingly powerful piece of software.