Welcome to why those types of "gee ain't it neat" effects usually are a bad idea on a page. I learned that lesson about six years ago when a page I had been maintaining by hand for two years was handed off to the client. In general, such 'trickery' is usually just bad accessibility, bad code, and completely unsustainable in the long term.
My advice: Pageloads aren't evil, split that out into a separate page if it's getting that long.
That way people can directly link to it (good for SEO), use normal navigation (forward/back) in relation to it, and it will probably save on bandwidth by not needing the extra code in the form of scripting. File it alongside scripted tags, animated banners, fancy fonts with illegible color contrasts, fixed height containers behind dynamic sized text, and all the other garbage that turns perfectly good website concepts into accessibility train wrecks that few people bother exploring deeper than the home page on.
Though... an APO element extending off the bottom SHOULD add the scrollbar -- if not then you've got something else on the page interfering with that like say... a min-height layout? Overflow:hidden on body maybe?
I'd have to see the site to say for sure... but normally an APO should NOT get cut off on the bottom or right -- only on the top or the left...
Could just be the page got too fancy for it's own good with some effects... May be time to cut it down a bit.