aproimage – you saved me 🙂 I had this problem before and I didn’t fix it, but this time I found your post. Messing up with style.css is the main reason template files are not visible in the dropdown list in the edit page view.
I was trying to create a menu based on your plugin but using background images assigned with unique_class through css (instead of text).
I modified your plugin and added link_wrap parameter which allows me to wrap links into tags like this: <a href=""><SPAN>navigation link</SPAN></a> and then set #nav li a span to display:none.
Some better way might be to actually display the images somehow (might be more SEO friendly ?) but this is just an idea.
Anyway this is really great plugin!