The problem is that Builder knows the root of the server but my application project is not on the root of server but on a folder embedded in it. So in order to make this work, just add a URL prefix to the project. Right click on the project and click on "SET URL Prefix":
Click on it and you will get the following dialog and fill out the FULL URL, I tried just the directory, but it did not work, maybe a bug in Builder. So put the FULL URL.
Hope this helps, enjoy!