We normally have \'Payload\' folder as root once we unarchive IPA files. However, suddenly Xcode has started creating IPAs with \'Applications\' fo
I have created .xarchive file using xcode 6.1 and then created .ipa file as per my answer here How to convert .xcarchive to .ipa for client to submit app to app store using Application Loader.
Now i have unarchieved my ipa file and it is having same folder structure as normal one, i.e. folder named "Payload" is available(no any Applications file). Also MDM is also working fine with that. Please check the way you have used, or else try this way.