Normally something like that is caused by a height="100%" in a table. I haven't had the problem for a while so I can't remember the exact circumstances of it. Anyway, I don't see any occurrence of the string "100%' on your pages so I don't think that can be the problem. It certainly is strange.
On a side note, you don't need to have two versions of your website. You should be able to have it dynamically resize with the size of the browser window. The way you have your content will fit into this scheme nicely. You have a nice small navigation bar on the left and basically pure text in the middle. That can conform to any browser size.