I am running into the same issue. I am currently adapting jquery Galleriffic slideshow to work with Image Gallery.
I want the link to point to http://holybasil.info/gallerifficpage/#image,
If I remove the base tag, all is well with the slideshow navigation, but not my template, particularly logging in to the admin.
relative to the base tag. Something, I don't know how to do at this time.