We have not heard of this problem before - so I wonder if perhaps you started your project from a template or by using the Custom tab in the New Document dialog (if you use Pro).
If you use the Blank template, then you will be asked to set up a project folder which will be the place where the Freeway file is saved and then the file will automatically use the Site Folder that is also located within that project folder.
However, starting a site as a Custom file you can start work on the file immediately without being prompted by Freeway to choose a project folder into which all the files will be saved. When you first publish the file by using Preview or Preview in Browser, Freeway will then ask you where you want to publish the files (this folder will be the site folder for the file) - so perhaps you chose the same folder as where you have saved the Freeway file?
Try going to File>Document Setup, click on the Select button, create a new folder on your hard disk and click Choose. This is the folder that the Freeway file will use as the site folder rather than publishing into the same folder as where the Freeway file is currently located.
To tidy things up I suggest you make an “archive” of the site to get everything in a logical structure. To do this, open the Freeway file, go to File>Save Archive, choose a name and location for where to save the archive folder then save it to your hard disk. Close the current Freeway file, open the archive folder and you will see the Freeway file has been saved into there, along with a Site Folder (which will currently be empty, though it will be populated with the site files when you publish the file) and a folder called Media (where any resources used in the site will be collated together and stored). If you open and work on the Freeway file in the archive folder, then it should all be fine from now on.
It would be interesting to know if, when you say “my new Mountain Lion Server”, whether you are using the Server version or the standard version of Mountain Lion.
We have run tests on the standard version of Mountain Lion and we can’t reproduce the same problems as you report, so anything more you can give us will help to see if this is a Mountain Lion issue or not.
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