Android : Android Studio intermittent ClassNotFoundException

I've already read serveral Q&A's from SO and did not found a solution.

My problem is: I run my app from AndroidStudio and get the error bellow, then I run gradlew clean installDebug and code works just fine (outside AS, with NO changes).

I did NOT forgot to include my activity into AndroidManifest.

10-13 13:36:18.261    1457-1457/my.package E/AndroidRuntime﹕ FATAL EXCEPTION: main
    Process: my.package, PID: 1457
    java.lang.RuntimeException: Unable to instantiate activity ComponentInfo{my.package/my.package.activity.MainActivity}: java.lang.ClassNotFoundException: Didn't find class "my.package.activity.MainActivity" on path: DexPathList[[zip file "/data/app/my.package-1.apk"],nativeLibraryDirectories=[/data/app-lib/my.package-1, /system/lib]]
            at android.app.ActivityThread.performLaunchActivity(ActivityThread.java:2110)
            at android.app.ActivityThread.handleLaunchActivity(ActivityThread.java:2233)
            at android.app.ActivityThread.access$800(ActivityThread.java:135)
            at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1196)
            at android.os.Handler.dispatchMessage(Handler.java:102)
            at android.os.Looper.loop(Looper.java:136)
            at android.app.ActivityThread.main(ActivityThread.java:5001)
            at java.lang.reflect.Method.invokeNative(Native Method)
            at java.lang.reflect.Method.invoke(Method.java:515)
            at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:785)
            at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:601)
            at dalvik.system.NativeStart.main(Native Method)
     Caused by: java.lang.ClassNotFoundException: Didn't find class "my.package.activity.MainActivity" on path: DexPathList[[zip file "/data/app/my.package-1.apk"],nativeLibraryDirectories=[/data/app-lib/my.package-1, /system/lib]]
            at dalvik.system.BaseDexClassLoader.findClass(BaseDexClassLoader.java:56)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:497)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:457)
            at android.app.Instrumentation.newActivity(Instrumentation.java:1061)
            at android.app.ActivityThread.performLaunchActivity(ActivityThread.java:2101)
            at android.app.ActivityThread.handleLaunchActivity(ActivityThread.java:2233)
            at android.app.ActivityThread.access$800(ActivityThread.java:135)
            at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1196)
            at android.os.Handler.dispatchMessage(Handler.java:102)
            at android.os.Looper.loop(Looper.java:136)
            at android.app.ActivityThread.main(ActivityThread.java:5001)
            at java.lang.reflect.Method.invokeNative(Native Method)
            at java.lang.reflect.Method.invoke(Method.java:515)
            at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:785)
            at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:601)
            at dalvik.system.NativeStart.main(Native Method)

I'm using Android Studio 0.8.12 and this is reproducible with real devices and emulator (Genymotion).

EDIT I've tried both "full path" and "class name only" into my AndroidManifest file to declare activities. And it still doesn't explain (IMHO) why it works via command line with gradle.