Could you please post links to the files and folders? When you use the Google Webmaster Tools interface to submit your sitemap, you will have to enter a complete URL to the sitemap.xml file there. It would be helpful if you could include in your reply an example of a page that appears on the map and yet does not exist in your site.
One thing that occurs to me here is that Freeway can, in general, get confused about files created by Actions. The symptoms of this include a lot of duplicate files, suffixed with -1, -3, etc. The cause of this is Freeway losing track of its own files (in its internal database) and then being conservative about overwriting any existing files on your Mac. (This is a nice thing, honestly.)
A quick way to test this assertion is to locate your local Site Folder on your Mac, and completely delete all contents within it. Then publish your site again. All files and folders will be re-generated automatically. See if you have the same problem in the Site Folder after the publish completes. If you don’t, then clear out your site’s home folder on your server and upload again. This should clear up the problem for you.
Make sure you have a backup before you delete files from your server, though. Any good SFTP application like Transmit or CyberDuck should be able to duplicate a folder in place on your server, and if all goes sideways, you can then delete the original and rename the copy and be back in business.
Walter
PS: Definitely use the built-in SFTP to upload to your server. Freeway tracks which files are “dirty” compared with the server, so you can be assured that everything that has changed will be updated on the server. Transmit can do this as well with its Synch service, but it is working at one remove from the truth. Freeway knows – with absolute certainty – which files it has modified.
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