No, I apologise; - if I hadn't butted in, Jimmy would have picked this up earlier and sorted it by now. Not the first time I've messed things up.
I'm not sure what's happening, I can't think why the pages are getting rewritten prior to uploading.
When you download the PowerCMS files (CMS201) and unzip it, then rename the 'Rename_this_folder_and_upload' to (say) 'cms', it is not possible (that I can see) for the actual code in the pages to be rewritten just by unzipping the folder and renaming the folder inside.
All I can think of now (though I suggest you go with whatever Jimmy advises) is that you avoid using Dreamweaver in any part of the process whatsoever; it may be that Dreamweaver is somehow messing it up (as well as me).
I always use a seperate ftp client to do the uploading, - a) because it's quicker, and b) because I can be sure that what goes up is unaffected by any Dreamweaver processes.
If you want to try that, a good (free) ftp client is filezilla. You can download a copy HERE
Install it, and when you run it create a new site by: File > Site Manager > New Site.
Have a look at the attached images for setting up your connection.
In the advanced Tab, (image 2) you put the default remote directory - if you're not sure what it is, leave it blank for now, you can put it in later.
If you look at image 3, you will see that you can navigate to where your site files are, and when you are there, your default remote directory shows in the 'Remote site' field above the right-hand pane.
Then in the lefthand pane (local files) you can right-click the folder you want to upload, and click 'upload' to transfer it to the remote folder (right-hand pane). - Image 4.
Even if you don't use it now, using a seperate ftp client is bound to be useful in the future.
Again, sorry for confusing the issue for you.