Add "Default Display Style - Set a different gallery-id for each WordPress Gallery" option. You can use "Gallery Images" style in WordPress Gallery even when using "Single Image" style.

auto-thickbox-options.php

@@ -84,6 +84,13 @@ jQuery(function($) {
 			<?php _e('Gallery Images', 'auto-thickbox'); ?> (<code>&lt;a href="image" rel="gallery-id">&lt;img />&lt;/a></code>)</label>
 		</td>
 	</tr>
+	<tr>
+		<th scope="row"></th>
+		<td>
+			<label><input type="checkbox" name="auto-thickbox-plus[wp_gallery]"<?php $this->checked($this->options['wp_gallery'], 'on'); ?> />
+			<?php _e('Set a different gallery-id for each WordPress Gallery', 'auto-thickbox'); ?> (<code>[gallery link="file"]</code>)</label>
+		</td>
+	</tr>
 	<tr>
 		<th scope="row"><?php _e('Auto ThickBox', 'auto-thickbox'); ?></th>
 		<td>
@@ -832,7 +839,7 @@ jQuery(function($) {
 		register_setting( 'auto-thickbox-plus-options', 'auto-thickbox-plus', array(&$this, 'options_callback') );
 	}
 
-	var $checkboxes_on = array('thickbox_text', 'auto_resize',
+	var $checkboxes_on = array('wp_gallery', 'thickbox_text', 'auto_resize',
 		'key_close_esc', 'key_close_enter',
 		'key_prev_angle', 'key_prev_left',
 		'key_next_angle', 'key_next_right',

auto-thickbox.php

@@ -159,6 +159,21 @@ class auto_thickbox {
 	} # styles()
 
 	function footer_scripts() {
+		if ( $this->options['wp_gallery'] == 'on') {
+?>
+<script type="text/javascript">
+/* <![CDATA[ */
+jQuery(function($) {
+	$('div.gallery').each(function() {
+		var id = $(this).attr('class').match(/galleryid-\d+/);
+		$(this).find('a.thickbox').attr('rel', id);
+	});
+});
+/* ]]> */
+</script>
+<?php
+		}
+
 		if ( $this->options['builtin_res'] == 'on') {
 			if ( version_compare('3.2', get_bloginfo('version')) > 0 ) {
 				$includes_url = includes_url();
@@ -429,6 +444,7 @@ SCRIPT;
 
 		$this->options_def = array(
 			'thickbox_style' => 'single',
+			'wp_gallery' => 'on',
 			'thickbox_text' => 'on',
 			'thickbox_target' => 'off',
 			'no_thickbox' => 'nothickbox no_thickbox ',