Reproduction steps:
1) Create new project
2) Export empty project with Gradle build
-- There are some changes which have to be done to the 'UnityPlayerActivity' class.
-- You can follow steps below or just download ConfiguredGradleBuilds.zip (link to OC cloud) with already configured gradle builds

3) Open exported build with Android Studio
4) Inside 'UnityPlayerActivity' class add:
LayoutInflater inflater = LayoutInflater.from(this);
View layout = inflater.inflate(R.layout.layout_test, mUnityPlayer, false);
FrameLayout.LayoutParams layoutParams = new FrameLayout.LayoutParams(ViewGroup.LayoutParams.MATCH_PARENT, ViewGroup.LayoutParams.MATCH_PARENT);
mUnityPlayer.addView(layout, layoutParams);

5) Import these classes (can be added by pressing alt+enter on errors, except 'layout', or manually) on top of a class:
import android.view.LayoutInflater;
import android.widget.FrameLayout;
import android.view.ViewGroup;
6) Add 'layout_test.xml' to the "BugReport/src/main/res/layout/" folder
7) Deploy application

Actual result: Button appears as soon as game launches and disappears on loading screen (Unity splash screen).
Expected result: Button appears as soon as game launches and stays for whole duration of the game.

Note: Also reproduced with ADT

Regression appeared in 5.6.0b3

Reproduced with:
5.6.0b3, 5.6.0b11, 2017.1.0a4

Unable to reproduce with:
5.5.2p3, 5.6.0b2

DUT:
Samsung Galaxy S6 Edge, Android 6.0.1
Samsung Galaxy S3, Android 4.3
LG G3, Android 5.0