the eCart code that should be above the doctype tag on your pages has been deleted.
Looks like Dreamweaver is deleting that code when you make changes to the template and update the pages.
You can prevent this from happening by converting your template to Theme using framework builder and using the theme on your pages instead of the template.
Using themes has the advantage of separating the page from the template. When you make changes to the template, you will no longer need to update the pages for the change to be applied, the template gets applied to the page at run time rather than having to apply the template to the page and re upload all files.
Another option to think about is to use the plugins to add the menu to the template. Create a new page, add the meny to the page and use Frmework builder plugins to add the menu.
We will be having a webinar this weekend on using Framework builder:
we will be covering topics such as plugins and themes to give a more comprehensive over view of using them.
there is also a tutorial here for using themes:
and this one is a general getting started guide for Framework builder that touches on using plugins: