Hello,
From what I understand from your problem, the issue is not of the IPv6, please test your app on an iPad, as if you closely look at the screenshots attached from Apple, they always test the apps on iPad, even if its only meant for iPhone, and if there is some over lapping of buttons, the app will not work, or call API function calls, which makes apple feel that the app is not Compatible with IPv6.
I hope you can test it on an iPad, and look for a solution, or ask your programmer to test it on iPad Simulator. Hope this helps :)
Best Regards,
Himanshi