Meanwhile, I was able to solve this problem. I have a button that starts navigation to the next FlipViewItem. However, this button has been placed in FlipViewItem.
With my setup (touch device) nothing worked. Then I tried to click the button with the mouse, and it worked. After I turned off UseTouchAnimationsForAllNavigation , it also worked using touch input. In my tests, I placed the button outside of FlipView, and it worked using animations.
Here's the problem: when the button is pressed, the navigation animation tries to start ( SelectedIndex installed correctly), but stopped because the user is blocking the animation while still touching the button. Thus, the navigation is canceled, and SelectionChanged reports the current page.
The solution is to set the ManipulationMode buttons to All . After that, you cannot flip FlipViewItem at the touch of a button, but the animation runs and works like a spell.
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