SettingsFlyout and InputPane, flyout closing unexpectedly

Question

So another one with my favourite InputPane/soft keyboard. I used an existing example to implement a SettingsFlyout with my app's settings. Worked great, but I needed a few textboxes there and thus a proper soft keyboard handling. Easy, I thought. I added a scrollviewer with IsTabStop = true as a child of a popup and added my UserControl as a content of a scrollviewer. I added the popup in run time to a visual tree of the page (as a child of a top level grid). All works fine, but about ~50% of time when the flyout is opened and I tap in it, does not matter if in a textbox, background or another control, popup closes. The next time it's okay. But then I change only the content of the scrollview to corresponding usercontrol. I set breakpoints at all places where I set IsOpen to false and also in my Closed event handler. It's not from me, in event handler I only see a transition from native code, not very helpful either. What do I have to do to make it work properly the first time? Any ideas? Thanks.