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I successfully got my app through Apple's checks but I performed one more step than you.
Perhaps the "Make ipa" does not use the changed config.xml file?
I edited the config.xml file and removed the lines for the capabilities I didn't require (e.g. push etc).
But, then I exported to Xcode and recompiled there (as I add advertising to the code).
Perhaps this is where the difference lies.
regards
Andy.
I did everything like you said, but did not export to xcode for compilation, exported as ipa right away, so I guess the ipa builder do not make use of this file. Perhaps support has an answer on this?
see my reply in post below.
Andy; What xcode version are you using? Did you use iAd for your app? any tips?
I'm using Xcode 5.0.2 in OSX Mountain Lion.
I used Google Admob SDK for my app.
If you want to see how, check my tutorial:
http://a70785.wix.com/parkermobileapp...
Awesome 
Bookmarked Going to create a free ad-version of my app as soon as it is accepted by appstore.
@Andy: can you ping me at a href="mailto:max@appery.io" rel="nofollow"max@appery.io/a. Would like to chat with you regarding: http://a70785.wix.com/parkermobileapp...