Index: wp-admin/includes/upgrade.php
===================================================================
--- wp-admin/includes/upgrade.php	(revision 6124)
+++ wp-admin/includes/upgrade.php	(working copy)
@@ -195,6 +195,9 @@
 	if ( $wp_current_db_version < 5539 )
 		upgrade_230();
 
+	if ( $wp_current_db_version < 6124 )
+		upgrade_230_old_tables();
+
 	maybe_disable_automattic_widgets();
 
 	$wp_rewrite->flush_rules();
@@ -693,6 +696,13 @@
 	$wpdb->show_errors();
 }
 
+function upgrade_230_old_tables() {
+	global $wpdb;
+	$wpdb->query('DROP TABLE IF EXISTS ' . $wpdb->prefix . 'categories');
+	$wpdb->query('DROP TABLE IF EXISTS ' . $wpdb->prefix . 'link2cat');
+	$wpdb->query('DROP TABLE IF EXISTS ' . $wpdb->prefix . 'post2cat');
+}
+
 function upgrade_old_slugs() {
 	// upgrade people who were using the Redirect Old Slugs plugin
 	global $wpdb;
Index: wp-includes/version.php
===================================================================
--- wp-includes/version.php	(revision 6124)
+++ wp-includes/version.php	(working copy)
@@ -3,6 +3,6 @@
 // This holds the version number in a separate file so we can bump it without cluttering the SVN
 
 $wp_version = '2.3-beta3';
-$wp_db_version = 6075;
+$wp_db_version = 6124;
 
 ?>