Android GCM with product flavors

I have GCM sample android gradle project. It works fine, when I add 2 flavors, push notifications stop working. My compile manifest (from app\build\intermediates\manifests\ex\debug) file is as follows:

<manifest xmlns:android="http://schemas.android.com/apk/res/android"
    package="com.flavor.app"
    <uses-permission android:name="com.flavor.app.permission.C2D_MESSAGE" />

    <permission
        android:name="com.flavor.app.permission.C2D_MESSAGE"
        android:protectionLevel="signature" />

        <receiver
            android:name="com.google.android.gcm.GCMBroadcastReceiver"
            android:permission="com.google.android.c2dm.permission.SEND" >
            <intent-filter>
                <action android:name="com.google.android.c2dm.intent.RECEIVE" />
                <action android:name="com.google.android.c2dm.intent.REGISTRATION" />

                <category android:name="com.flavor.app" />
            </intent-filter>
        </receiver>

        <service android:name="com.ex.app.GCMIntentService" />
        <service
            android:name="com.ex.app.AppLocationService"
            class=".AppLocationService" >
            <intent-filter>
                <action
                    android:name=".AppLocationService"
                    android:value=".AppLocationService" />
            </intent-filter>
        </service>

What should I do to solve this problem? please help.

UPD1. I am using gradle v.0.12+. I think my final manifest file looks fine, GCMRegistrar.checkManifest(this); - no errors, but GCMRegistrar.isRegistered(this) is always false. =(

UPD2. My first flavor project with the original package name (as a project in the master branch) works fine, but the second flavor with the changed package doesn't work (the registrationId for push is still empty), but the manifest file All permissions in are correct.