@thebugnut, didi you figure out what was causing this problem?
This warning indicated that you are adding a file to a folder where the file name already exists.
For example, if your website is www.mysite.com/ the first page you add will have an empty field in the “folder” setting and “index.html” or “index.php” in the “Filename” setting.
Having and empty folder name will place the file in the root directory of your site. In this example, the URL would be www.mysite.com/index.html or www.mysite.com/index.php
If you add a new page your project RapidWeaver will automatically create a Folder and name it “page” with a Filename of “index.html” or “index.php”. If you remove the Folder name without adding a new one then it will recognize that you are you are trying to add a file to a folder that already has that file name.
You can resolve this by changing the file name to something like “about.html” or you can change the folder the file id published to.
I know this is an old post and home that you have already resolved this. However, I figured it worth responding in case someone else comes across this looking for a solution in the future.