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I have answered your email in support, but for anyone else who comes across this thread.
The reason I think this is happening, is because of the number of pages in your menu. You can add as many pages to your site as you like. However, different styles support a different number of pages in the menu. If you use a style with horizontal navigation (with the menu along the top) after a certain number of pages the menu links will disappear or start running into the body region of the page. If you have many pages it is best to select a style with vertical navigation (with the menu down the side). The other alternative is to divide your site into categories and create subpages. Here is a link to a tutorial that will explain how to do this: http://www.synthasite.com/tutorials/c....
You could also try making the names of your pages in the menu shorter. This will give you more room.