Hi,
I don't think it has something to do with the SEF URL. It just can't be related to that. Because the slideshow is working based on where the slideshow module is published.
Find this Module:
Background Slideshow in the module position of:
backgroundslideshow
Double check that; module is only published on Homepage. Then the slideshow should be activated only on Homepage, not the other pages.
Like this:
Attachment ScreenShot2014-03-28at8.03.23AM.png not found
Regards,
Support