It's really a common template problem...
You need to add a container div that wraps your menu. Open your template's index.php file and look for the place where the menu is called. It should be something like:
<div id="nav">***menu code here***</div>
So, add a "wrapper" div, like so:
<div id="menu-container"><div id="nav">***menu code here***</div></div>
And then in your template's CSS file (template_css.css), add the following code snippet:
This should fix any issues.