Yep, I have had the same problem with some of my skins. You'll notice that if you open your browser up to full screen mode, the sidebar moves up into place on the right, where it should be (assuming your screen resolution is above 800x600).

To fix this, you'll need to adjust your column sizes, so that they always fit beneath the 'page' width that is specified. Try adjusting your browser size down to 800x600, and then in your CSS file, adjust your column widths so that they always fit within the maximum width that you've specified for that image at the top. That way, no matter what size someone's browser is set to, that navigation column will always be on the right.

You & I aren't alone in this problem, its one that comes up fairly frequently on the boards. Here are some threads that may help.
[url=http://forums.b2evolution.net/viewtopic.php?p=14173]Sidebar pushed down in IE[/url]
[url=http://forums.b2evolution.net/viewtopic.php?t=3944]IE vs. Firefox: Sidebar problems[/url]
[url=http://forums.b2evolution.net/viewtopic.php?t=2476]CSS for both IE and Firefox[/url]
[url=http://forums.b2evolution.net/viewtopic.php?t=2063]How to resize right column?[/url]

And of course, come back with questions if you get stuck.

Hope That Helps,
Chris