I just had to do the same thing again. After the automatic plugin update the settings page said “No banner found” but once I manually deactivated and reactivated the plugin it gave me the “This WP Bannerize release has a different Database Table struct. WP Bannerize has found an old Database Table. Do you want convert old struct for this release?” message.
I’m running WP 3.0.1 on CentOS Linux hosted by Webfaction with a private PHP 5.2.9 stack.