Not sure why that would happen.
send a copy of the original template, the new template, the index page and one of the other pages that should not have been updated so i can take a look please.
Your friends over here at WebAssist! These Dreamweaver extensions will assist you in building unlimited, custom websites.
These out-of-the-box solutions provide you proven, tested applications that can be up and running now. Build a store, a gallery, or a web-based email solution.