Thanks for the login. I don't have an immediate solution but I did find the problem.
Look at the last line in your body tag on a page that's having issues. Looks like this:
<div id="roksearch_results" style="position: absolute; top: 3595px; left: 235px; visibility: hidden; opacity: 0;"></div>
You'll notice the very high "top:" number. This line is generated by RokSearch to appropriately display search results. Try doing a search and you'll see the page re-sizes correctly.
This high number is probably generated for one of two reasons (or both).
1) jCarousel is using position:relative tags for each clip it displays. This tag will adjust (move) the position of an element but will not eliminate the original space it occupied. You can break the div container around your carousel and all the clips will line up vertically. You'll see it fills the "black" space perfectly. The positions surrounding jCarousel contain this "extra" space but RocSearch is still recognizing it for some reason.
2) Although the jQuery script jCarousel uses is running in jQuery.noConflict(), it doesn't guarantee mootools won't have a conflict. I know you can use some functions in both libraries together, I'm just not familiar with jCarousel enough to say it is compatible with everything in the Nebulae template using mootools.
You can make a quick fix by dropping RokSearch or jCarousel. You may be able to tweak one of them as to overcome the conflict.