I've updated the main plugin and had no issues. The custom taxonomy and roles are not updating, although the permissions are correct (owned by apache) and the admin indicates that the plugin was installed successfully. I've even done it manually via SFTP and then reset permissions to apache and and the plugins page still prompts me for an update for these two (taxonomies and roles). Seems like a bug, but I'm not sure. It's the only two plugins I have not been able to update.