The menu methods (onCreateOptionsMenu, onPrepareOptionsMenu, onOptionsItemSelected) are never invoked for both controllers. Also, when pressing the default back button, the controller is popped but it's view still lingers on screen.

DemoActivity.java

package com.kevelbreh.fit.demo;

import android.os.Bundle;
import android.support.annotation.NonNull;
import android.support.v7.app.AppCompatActivity;
import android.support.v7.widget.Toolbar;
import android.view.LayoutInflater;
import android.view.Menu;
import android.view.MenuInflater;
import android.view.MenuItem;
import android.view.View;
import android.view.ViewGroup;

import com.bluelinelabs.conductor.ChangeHandlerFrameLayout;
import com.bluelinelabs.conductor.Conductor;
import com.bluelinelabs.conductor.Router;
import com.bluelinelabs.conductor.RouterTransaction;
import com.bluelinelabs.conductor.changehandler.FadeChangeHandler;
import com.bluelinelabs.conductor.rxlifecycle.RxController;
import com.kevelbreh.fit.R;

import butterknife.BindView;
import butterknife.ButterKnife;
import butterknife.OnClick;
import timber.log.Timber;

public class DemoActivity extends AppCompatActivity {

    @BindView(R.id.toolbar) Toolbar toolbar;
    @BindView(R.id.controller_container) ChangeHandlerFrameLayout container;

    private Router router;

    public void onCreate(Bundle savedInstanceState) {
        super.onCreate(savedInstanceState);

        setContentView(R.layout.activity_home);
        setSupportActionBar(toolbar);
        ButterKnife.bind(this);

        router = Conductor.attachRouter(this, container, savedInstanceState);
        if (!router.hasRootController()) {
            router.setRoot(new DemoActivity.HomeController());
        }
    }

    @Override
    public void onBackPressed() {
        if (!router.handleBack()) {
            super.onBackPressed();
        }
    }

    // Menu methods never get invoked.
    public static class HomeController extends RxController {

        @OnClick(android.R.id.button1)
        public void onButtonClicked() {
            getRouter().pushController(RouterTransaction.builder(new DemoActivity.SubController())
                    .pushChangeHandler(new FadeChangeHandler())
                    .popChangeHandler(new FadeChangeHandler())
                    .build());
        }

        public HomeController(Bundle bundle) {
            super(bundle);
            setHasOptionsMenu(true);
        }

        public HomeController() {
            super(null);
            setHasOptionsMenu(true);
        }

        @NonNull @Override
        protected View onCreateView(@NonNull LayoutInflater inflater, @NonNull ViewGroup container) {
            View v = inflater.inflate(R.layout.controller_home, container);
            ButterKnife.bind(this, v);
            return v;
        }

        @Override
        public void onCreateOptionsMenu(Menu menu, MenuInflater inflater) {
            super.onCreateOptionsMenu(menu, inflater);
            inflater.inflate(R.menu.menu_home, menu);
            Timber.d("onCreateOptionsMenu");
        }

        @Override
        public void onPrepareOptionsMenu(Menu menu) {
            super.onPrepareOptionsMenu(menu);
            Timber.d("onPrepareOptionsMenu");
        }

        @Override
        public boolean onOptionsItemSelected(MenuItem item) {
            Timber.d("onOptionsItemSelected %s", item.getItemId());
            return super.onOptionsItemSelected(item);
        }
    }

    // Menu methods never get invoked.
    public static class SubController extends RxController {

        public SubController(Bundle bundle) {
            super(bundle);
            setHasOptionsMenu(true);
        }

        public SubController() {
            super(null);
            setHasOptionsMenu(true);
        }

        @NonNull @Override
        protected View onCreateView(@NonNull LayoutInflater inflater, @NonNull ViewGroup container) {
            return inflater.inflate(R.layout.controller_workout_manage, container);
        }

        @Override
        public void onCreateOptionsMenu(Menu menu, MenuInflater inflater) {
            super.onCreateOptionsMenu(menu, inflater);
            inflater.inflate(R.menu.menu_workout_manager, menu);
            Timber.d("onCreateOptionsMenu");
        }

        @Override
        public void onPrepareOptionsMenu(Menu menu) {
            super.onPrepareOptionsMenu(menu);
            Timber.d("onPrepareOptionsMenu");
        }

        @Override
        public boolean onOptionsItemSelected(MenuItem item) {
            Timber.d("onOptionsItemSelected %s", item.getItemId());
            return super.onOptionsItemSelected(item);
        }
    }
}