Ashley I have a thread going about this problem over at the phonegap build forums. The last response from Amir who is from the phonegap build team was that he suspected the c2runtime.js file to be the reason for the app making the location permission request at start up. I'm not sure that is the case but I would be very grateful if you could have a look at this issue.
let me know if you have some time to look into this and if you need anything, files, more info etc.
Here is the thread at the phonegap build community:
http://community.phonegap.com/nitobi/to ... tton&reply[id]=15227901#reply_15227901
I'm attaching a screen shot of the project, not sure what good it will do but at least it can provide some context.