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We've been investigating the recent problems with Whatsapp and Freedome on devices with iOS 9.
Based on our investigations, Whatsapp crashes each time in the background when a push notification arrives and Freedome is running. Because of this, the incoming message will not be displayed.
We will notify Whatsapp about this and provide them with information about the crashing, as this issue seems to be something that cannot be fixed within Freedome.
To keep you all updated on this issue, the fix has been submitted for Apple app store review and it depends on the review time a lot. However, we are hoping to have the fix out before Christmas.