In this case is not necessary the use of “%[num]$s” for the function printf() “%s” is enough. And the problem is the 5th parameter. So just replace the line 289 for this:
printf( __( 'There is a new version of %s available. <a href="%s" class="thickbox" title="%s">View version %s details</a> or <a href="%s" class="update-link">update now</a>.' ),
$plugin_name, esc_url( $details_url ), esc_attr( $plugin_name ), $r->new_version, wp_nonce_url( self_admin_url( 'update.php?action=upgrade-plugin&plugin=' ) . $file, 'upgrade-plugin_' . $file ) );
