Native scrolling issue - popup pushed too far up

I recently updated the Ionic version in my app from 1.0.0-rc.2 to 1.2.4. I’m now using native scrolling on Android, and everything works perfectly, except from one thing. I have popups that contain inputs and when the popup comes up and the input is focused on, the popup gets pushed up too far. See image:

What happens is, the keyboard comes up and the popup goes to the right place, but a second later it gets pushed up further out of the view.

I tried several other version of Ionic with native scrolling enabled for Android and it works fine on 1.0.0-rc.2 but anything later and it starts happening. Any ideas as to how to fix this?