Only in .: flashtheme.patch
diff -urp ./slideshowpro.module ../slideshowpro_patched/slideshowpro.module
--- ./slideshowpro.module	2009-02-27 11:14:48.000000000 +1000
+++ ../slideshowpro_patched/slideshowpro.module	2009-02-27 11:16:32.000000000 +1000
@@ -56,6 +56,16 @@ function slideshowpro_theme($existing, $
         'title_caption' => NULL,
       ),
     ),
+    'slideshowpro_flash' => array(
+      'file' => 'slideshowpro.theme.inc',
+      'arguments' => array(
+        'id' => NULL,
+        'width' => NULL,
+        'height' => NULL,
+        'flash_vars' => NULL,
+        'path' => NULL,
+      ),
+    ),
     'slideshowpro_embed' => array(
       'file' => 'slideshowpro.theme.inc',
       'arguments' => array(
@@ -212,15 +222,7 @@ function slideshowpro_embed($args) {
   if (isset($args['height'])) {
     $height = ' height="'. $args['height'] .'" ';
   }
-  
-  return theme('slideshowpro_embed', 
-    '<object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" 
-      codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=8,0,0,0" '. $width .' '. $height .' id="ssp-player-'. $id .'" align="middle">
-      <param name="allowScriptAccess" value="sameDomain" />
-      <param name="FlashVars" value="'. $flash_vars .'" />
-      <param name="movie" value="'. base_path() . slideshowpro_path_to_ssp() .'" />
-      <param name="quality" value="high" />
-      <param name="bgcolor" value="#ffffff" />
-      <embed FlashVars="'. $flash_vars .'" src="'. base_path() . slideshowpro_path_to_ssp() .'" quality="high" bgcolor="#ffffff" '. $width .' '. $height .' name="ssp-player-'. $id .'" align="middle" allowScriptAccess="sameDomain" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" /> 
-    </object>', $id);
+
+  $output = theme('slideshowpro_flash', $id, $width, $height, $flash_vars, base_path() . slideshowpro_path_to_ssp());
+  return theme('slideshowpro_embed', $output, $id);
 }
\ No newline at end of file
diff -urp ./slideshowpro.theme.inc ../slideshowpro_patched/slideshowpro.theme.inc
--- ./slideshowpro.theme.inc	2009-02-27 11:14:48.000000000 +1000
+++ ../slideshowpro_patched/slideshowpro.theme.inc	2009-02-27 11:16:33.000000000 +1000
@@ -104,6 +104,22 @@ function theme_slideshowpro_xml_image(&$
 }
 
 /**
+ * Theme flash output.
+ */
+function theme_slideshowpro_flash($id, $width, $height, $flash_vars, $path) {
+  return '<object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000"
+      codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=8,0,0,0" '. $width .' '. $height .' id="ssp-player-'. $id .'" align="middle">
+      <param name="allowScriptAccess" value="sameDomain" />
+      <param name="FlashVars" value="'. $flash_vars .'" />
+      <param name="movie" value="'. $path .'" />
+      <param name="quality" value="high" />
+      <param name="bgcolor" value="#ffffff" />
+      <param name="wmode" value="transparent" />
+      <embed FlashVars="'. $flash_vars .'" src="'. $path .'" quality="high" wmode="transparent" bgcolor="#ffffff" '. $width .' '. $height .' name="ssp-player-'. $id .'" align="middle" allowScriptAccess="sameDomain" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" />
+    </object>';
+}
+
+/**
  * Theme output.
  */
 function theme_slideshowpro_embed($output, $id) {