I notice occasionally when I am installing module updates I get the error saying that Plugin Manager could not connect via ftp (I'm assuming it's the server timing out or something). When this happens and only some of the module updates are installed, all of the modules (even the ones that were already installed) stay in the queue, and won't go away no matter what I do. The only way that I have found to get rid of them is to uninstall the plugin manager module and then reinstall it. As you can imagine, this gets very annoying after you have to do it multiple times.