To fix the problem with SEO you will have to give the link of your site in header.swf and in photos.xml. To create header.swf use header.fla which is included on the download (for commercial templates).
Example 1
If your site is www.yoursite.com and you are using the template ju_business open header.fla with the flash program you have and you should change the link on Actions
from
templates/ju_business/photos.xml
to http://www.yoursite.com/templates/ju_business/photos.xml
In photos.xml change the link for all the images from
templates/ju_business/images/header........
to http://www.yoursite.com/templates/ju_business/images/header........