Yes, that make perfect sense. That is a common effect when you are using the Website Wizard. In some cases this can be fixed, some cases not. However, we would need a URL for your site, so we could provide a solution, if there is one.
Right now, at 800x600 visitors need to scroll right to see your navigation. I assume it will be just about right at 1024. Of course it would be nice if it would just fit any screen, but usually it is better to put some upper limit on width. Making sure a design works well in both 800 and 1200 requires more effort on your part. Besides which, most printers (at least the cheap ones I get to use) are in trouble with pages that get wider than 640.
As I said before, some of the Wizard Themes and Layouts can be made to automatically adjust to different screen sizes. Unfortunately, the one you have picked is one that can't be adjusted easily. That particular Theme is table based, and the content areas have very specific widths. Some are defined in the HTML and some in the CSS. It's possible that it could be done, but it would take a lot of work and it's unknown whether the graphics are flexible enough to let it work well.
