I was not able to reproduce a similar problem using Dreamweaver CS5 after installing the 11.0.3 Dreamweaver update. The checkout pages created by the checkout wizard did not have the code order problems that you mentioned.
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.