I initially created a web app (HTML, CSS, jQuery) without PhoneGap or Cordova. I used PhoneGap Build to build the app. Everything worked as expected.
However, I then installed PhoneGap, and adjusted my project's structure to work with PhoneGap. Now my config.xml file lives at the root, and the app lives in www.
I also used the config.xml file that PhoneGap creates when using the CLI, and removed the config.xml file I initially created when using PhoneGap Build's settings.
Since doing this, it seems that PhoneGap Build does not respect my config.xml file.
I've tried the following:
- Adding the 
config.xmlfile to thewwwdirectory in addition to keeping it at therootlevel. - Only keeping the 
config.xmlfile in thewwwdirectory. - Using the original 
config.xmlfile I created with PhoneGap Build in both thewwwandrootdirectories. 
Also, I am running PhoneGap 5.0.0-0.28.1. However, on PhoneGap Build it says I'm running 3.3.0
                        
@Stephen, On the versioning, you are likely setting your Phonegap Build version in your config.xml.
The issue you have with the actual location of the config.xml is a bug. I recently added this to the Google group. The bug is #522. It appears your bug is a variation on this same bug.