Thanks for mentioning the $.mobile.hashListeningEnabled = false; function, which helped me in the list problem concerning the IOS9, still Vinicius replied on another topic:
Phonegap 5.2.0 + jquery mobile 1.4.5 + xcode 6 or 7, resolved the problems.
I did not test it yet.
But what concerns me is the new IOS 9 hacking, is the app that is built on appery as IPA accepted by the Apple store or we need to download the xcode source and build it again using the xcode ?? I am afraid of getting an email that the app has been removed. Anyone has any info about it ?!