I recently released a new version of my configurable tag cloud plugin. In the new version, I moved from a single file in the plugins directory for the plugin to multiple files in a directory of their own. If you manually update the plugin via ftp upload, the update goes fine, but if you use the automated upgrade feature from the plugins menu, it creates a folder named "configurable-tag-cloud-widget" that contains the plugin folder, readme file, and screenshots. This causes the plugin to disappear from the plugins list, as WordPress can't find the plugin in the sub-directory.
Is there some way to fix this issue, so the users of my plugin can update automatically without worrying about the plugin disappearing?