To fix the problem with SEO you will have to give the link of your site in header.swf and in photos.xml (images.xml). To create header.swf use header.fla.

Example

If your site is www.mysite.com and you are using the template mx_joomla1 then open header.fla with your flash program and change the link on Actions
 
from
templates/mx_joomla1/images/photos.xml
to
http://www.mysite.com/templates/mx_joomla1/images/photos.xml

In photos.xml change the link for all the images from

templates/mx_joomla1/images/header/header........
to
http://www.mysite.com/templates/mx_joomla1/images/header/header........