Well, the disable part works...

Auto enable is still a bit trigger happy.  But, bugs worked out, might
try a method of detection that uses root...

app/src/main/java/com/topjohnwu/magisk/AutoRootFragment.java

@@ -29,13 +29,11 @@ public class AutoRootFragment extends ListFragment {
     private ApplicationAdapter listadaptor = null;
     public ListView listView;
     public SharedPreferences prefs;
-    private View view;
     List<String> arrayList;
 
     @Override
     public View onCreateView(LayoutInflater inflater, ViewGroup container, Bundle savedInstanceState) {
-        view = inflater.inflate(R.layout.auto_root_fragment, container, false);
+        return inflater.inflate(R.layout.auto_root_fragment, container, false);
-        return view;
     }
 
     @Override
@@ -49,7 +47,7 @@ public class AutoRootFragment extends ListFragment {
             Set<String> set = new HashSet<String>();
             set.add("com.google.android.apps.walletnfcrel");
             editor.putStringSet("autoapps", set);
-            editor.commit();
+            editor.apply();
         }
         new LoadApplications().execute();
     }

app/src/main/java/com/topjohnwu/magisk/MonitorService.java

@@ -1,7 +1,6 @@
 package com.topjohnwu.magisk;
 
 import android.app.AppOpsManager;
-import android.app.Fragment;
 import android.app.NotificationManager;
 import android.app.PendingIntent;
 import android.app.Service;
@@ -11,7 +10,7 @@ import android.content.Context;
 import android.content.Intent;
 import android.content.SharedPreferences;
 import android.os.Build;
-import android.os.CountDownTimer;
+import android.os.Handler;
 import android.os.IBinder;
 import android.os.Process;
 import android.preference.PreferenceManager;
@@ -32,25 +31,10 @@ public class MonitorService extends Service
 {
 
     private static final String TAG = "Magisk";
-    private UsageStatsManager mUsageStatsManager;
+    Handler handler = new Handler();
-    private SharedPreferences prefs;
     private Boolean disableroot;
     private Boolean disablerootprev;
-    public static boolean isRecursionEnable = false;
+    private Boolean stopauto;
-    private NotificationManager mNotifyMgr;
-    private CountDownTimer timer = new CountDownTimer(1000, 1000) {
-
-        @Override
-        public void onTick(long millisUntilFinished) {
-
-        }
-
-        @Override
-        public void onFinish() {
-            CheckProcesses();
-
-        }
-    }.start();
 
     @Nullable
     @Override
@@ -60,46 +44,111 @@ public class MonitorService extends Service
 
     @Override
     public int onStartCommand(Intent intent, int flags, int startId) {
-        if (!intent.hasExtra("disable")) {
+            new Thread(() -> {
-
+                checkProcesses.run();
-
-            new Thread(new Runnable() {
-                @Override
-                public void run() {
-                    // DO your work here
-                    // get the data
-                    timer.start();
-                }
             }).start();
 
-
             return START_STICKY;
-        } else return STOP_FOREGROUND_REMOVE;
-    }
 
+    }
 
     @Override
     public void onDestroy() {
         Log.d(TAG, "Destroyah!");
-        android.os.Process.killProcess(android.os.Process.myPid());
         super.onDestroy();
+
     }
 
+    private Runnable checkProcesses = new Runnable() {
+        @Override
+        public void run() {
+
+            SharedPreferences prefs = PreferenceManager.getDefaultSharedPreferences(getApplicationContext());
+            if (prefs.getBoolean("autoRootEnable", false)) {
+
+                Set<String> set = prefs.getStringSet("autoapps", null);
+
+                if (set != null) {
+                    disableroot = getStats(set);
+
+                }
+                if (disableroot != disablerootprev) {
+                    int counter = 0;
+                    String rootstatus = (disableroot ? "disabled" : "enabled");
+                    if (disableroot) {
+                        Shell.su("setprop magisk.root 0");
+                        if (Shell.sh("which su").contains("su")) {
+                            Shell.su(("setprop magisk.root 0"));
+                        }
+                        if (Shell.sh("which su").contains("su")) {
+                            Shell.su(("setprop magisk.root 0"));
+                        }
+                        if (Shell.sh("which su").contains("su")) {
+                            Shell.su(("setprop magisk.root 0"));
+                        }
+                    } else {
+                            counter +=1;
+                            if (counter >=3) {
+                                Shell.su("setprop magisk.root 1");
+                                counter = 0;
+                            }
+                        }
+//                    Shell.su((disableroot ? "setprop magisk.root 0" : "setprop magisk.root 1"));
+
+                    NotificationManager mNotifyMgr = (NotificationManager) getSystemService(NOTIFICATION_SERVICE);
+                    NotificationCompat.Builder mBuilder;
+                    mNotifyMgr.cancelAll();
+                    if (disableroot) {
+
+                        Intent intent = new Intent(getApplication(), WelcomeActivity.class);
+                        intent.putExtra("relaunch", "relaunch");
+                        PendingIntent pendingIntent = PendingIntent.getActivity(
+                                getApplicationContext(),
+                                0,
+                                intent,
+                                PendingIntent.FLAG_UPDATE_CURRENT);
+
+                        mBuilder =
+                                new NotificationCompat.Builder(getApplicationContext())
+                                        .setSmallIcon(disableroot ? R.drawable.ic_stat_notification_autoroot_off : R.drawable.ic_stat_notification_autoroot_on)
+                                        .setContentIntent(pendingIntent)
+                                        .setContentTitle("Auto-root status changed")
+                                        .setContentText("Auto root has been " + rootstatus + "!  Tap to re-enable when done.");
+
+                    } else {
+                        mBuilder =
+                                new NotificationCompat.Builder(getApplicationContext())
+                                        .setAutoCancel(true)
+                                        .setSmallIcon(disableroot ? R.drawable.ic_stat_notification_autoroot_off : R.drawable.ic_stat_notification_autoroot_on)
+                                        .setContentTitle("Auto-root status changed")
+                                        .setContentText("Auto root has been " + rootstatus + "!");
+                    }
+// Builds the notification and issues it.
+                    int mNotificationId = 1;
+                    mNotifyMgr.notify(mNotificationId, mBuilder.build());
+
+                }
+                disablerootprev = disableroot;
+                Log.d(TAG,"Root check completed, set to " + (disableroot ? "disabled" : "enabled"));
+
+
+            }
+            handler.postDelayed(checkProcesses, 1000);
+        }
+
+    };
+
     private boolean getStats(Set<String> seti) {
         if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.M) {
             boolean inStats = false;
-            UsageStatsManager lUsageStatsManager = (UsageStatsManager) getSystemService(Context.USAGE_STATS_SERVICE);
             if (seti != null) {
                 ArrayList<String> statList = new ArrayList<>(seti);
                 for (int i = 0; i < statList.size(); i++) {
                     if (isAppForeground(statList.get(i))) {
                         inStats = (isAppForeground(statList.get(i)));
                     }
-
                 }
-
                 return inStats;
-
             }
             Log.d(TAG, "SDK check failed.");
         }
@@ -109,19 +158,14 @@ public class MonitorService extends Service
     protected boolean isAppForeground(String packageName) {
         UsageStatsManager usageStatsManager = (UsageStatsManager) getSystemService(Context.USAGE_STATS_SERVICE);
         long time = System.currentTimeMillis();
-
         List<UsageStats> stats = usageStatsManager.queryUsageStats(UsageStatsManager.INTERVAL_DAILY, time - 1000 * 10, time);
-
+        String topPackageName = "";
-        String topPackageName = new String();
-
         if (stats != null) {
             SortedMap<Long, UsageStats> mySortedMap = new TreeMap<>();
-
             for (UsageStats usageStats : stats) {
                 mySortedMap.put(usageStats.getLastTimeUsed(), usageStats);
             }
-
+            if (!mySortedMap.isEmpty()) {
-            if (mySortedMap != null && !mySortedMap.isEmpty()) {
                 topPackageName = mySortedMap.get(mySortedMap.lastKey()).getPackageName();
             }
         }
@@ -129,62 +173,6 @@ public class MonitorService extends Service
         return topPackageName.equals(packageName);
     }
 
-    private void CheckProcesses() {
-        prefs = PreferenceManager.getDefaultSharedPreferences(getApplicationContext());
-        if (prefs.getBoolean("autoRootEnable", false)) {
-
-            Set<String> set = prefs.getStringSet("autoapps", null);
-
-            ArrayList<String> arrayList = null;
-            if (set != null) {
-                disableroot = getStats(set);
-
-            }
-            if (disableroot != disablerootprev) {
-                String rootstatus = (disableroot ? "disabled" : "enabled");
-                Shell.su((disableroot ? "setprop magisk.root 0" : "setprop magisk.root 1"));
-                mNotifyMgr = (NotificationManager) getSystemService(NOTIFICATION_SERVICE);
-                NotificationCompat.Builder mBuilder;
-                mNotifyMgr.cancelAll();
-                if (disableroot) {
-                    timer.cancel();
-                    this.stopSelf();
-                    Intent intent = new Intent(this, WelcomeActivity.class);
-                    intent.putExtra("relaunch", "relaunch");
-                    PendingIntent pendingIntent = PendingIntent.getActivity(
-                            this,
-                            0,
-                            intent,
-                            PendingIntent.FLAG_UPDATE_CURRENT);
-
-                    mBuilder =
-                            new NotificationCompat.Builder(this)
-                                    .setSmallIcon(disableroot ? R.drawable.ic_stat_notification_autoroot_off : R.drawable.ic_stat_notification_autoroot_on)
-                                    .setContentIntent(pendingIntent)
-                                    .setContentTitle("Auto-root status changed")
-                                    .setContentText("Auto root has been " + rootstatus + "!  Tap to re-enable when done.");
-
-                } else {
-                    mBuilder =
-                            new NotificationCompat.Builder(this)
-                                    .setAutoCancel(true)
-                                    .setSmallIcon(disableroot ? R.drawable.ic_stat_notification_autoroot_off : R.drawable.ic_stat_notification_autoroot_on)
-                                    .setContentTitle("Auto-root status changed")
-                                    .setContentText("Auto root has been " + rootstatus + "!");
-                }
-// Builds the notification and issues it.
-                int mNotificationId = 001;
-                mNotifyMgr.notify(mNotificationId, mBuilder.build());
-
-            }
-            disablerootprev = disableroot;
-
-
-            Log.d(TAG, "Check Processes finished, result is " + disableroot + " and settings say we should be " + prefs.getBoolean("autoRootEnable", false));
-            timer.start();
-        }
-    }
-
     private boolean hasUsagePermission() {
         AppOpsManager appOps = (AppOpsManager)
                 getSystemService(Context.APP_OPS_SERVICE);
@@ -193,6 +181,5 @@ public class MonitorService extends Service
         return mode == AppOpsManager.MODE_ALLOWED;
     }
 
-
 }