This happens because it uses a column layout where left and right are positioned using absolute positioning. Things positioned using absolute positioning are not in the flow of the document, so in this case it is only the center content which pushes the footer down. So if you have less content in the center than the side it gets out of whack. The only real solution is to re-work that skin to use float based column layout instead of absolute positioning.
Unfortunately I have so many things to do that fixing this is a very very low priority for me.