i had problems with the slideshow and thickbox not working although gallery grids were fine.
firstly make sure your wp_head and wp_footer calls are in place in your theme (usually in the header and footer elements) otherwise things like the thickbox js file don’t get called.
in my case my slideshow wasn’t working because i had a clash with a call to an older jquery js file in one of my theme files. so check your jquery versions and calls (check you haven’t got 2 calls to jquery in your compiled pages).
the flash imagerotator location issue can be a red herring. i’m not using the flash version for the slideshow so don’t have anything in the URL field for the imagerotator. lots of the support on this focus on this file location.