Nextgen Gallery scroll images stacking up!

Hi, I have installed the both Nextgen gallery and scroll as plugins, I have the gallery working fine when I use WP default themes, however when I revert to my own custom theme the images stack on top of each other with the thumbnail images in place, but unclickable, its almost as if the javascript is not working?

I have tried to strip my theme back to its bare bones, but I cant figure out what my theme is missing that the WP defaults have, any point in the right direction would be greatly appreciated.