There are basically 2 approaches to column layout as used in skins included with mojoportal, some skins use one approach and some use the other.
The first approach uses absolute positioning for the left and right sides. One of the advantages of this approach is that it can be better for SEO (Search Engine Optimization) because with absolute postiiong you can put the left and right side content at the bottom of the page physically, allowing the center which presumably has the most important content to occur sooner in the rendered markup. The disadvantage of this approach is that things that are positioned absolutely are taken "out of the flow" of the page. Therefore left and right side content do not push the footer down, only center content pushes the footer down, so if there is more content inj left or right than in center, the footer rises up to the bottom of the center. This is the problem you describe. I have no solution to offer other than change to a skin that uses the other layout type or harvest the layout approach from another skin and create a custom one that looks like the one you are using but has a different layout.
The second approach for column layout used in some mojoportal skins is to float everything left and use margins to separate them. This approach does not have the problem with the footer, but it also does not have the SEO advantage. The left column comes first followed by middle and right.
I moved this post from the bug report forum where you originally posted it because I do not see it as a bug but as a tradeoff of pros and cons in design. I also moved it to this forum becuase it will be easier to find for anyone else who has the same question.
Hope it helps,