You can also backup and restore individual tables using phpMyAdmin.
If you are using wassup, that could be your problem. I stopped using it because it is an incredible resource pig. If you are using that plugin and you have not changed the default settings, it keeps building history forever and tables get very large. You can delete the history in the configuration screen.
"Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote." -- Benjamin Franklin