Chainfire’s most recent Systemless Root is the preferred rooting method for Android Marshmallow devices, but some root apps do not recognize Systemless root, hence stop working. However, there is a simple workaround to fix this issue. If an app does not recognize root access on your device (if you used Systemless SU for rooting), just follow the below simple steps.
Systemless root is the most recent development by Chainfire. The benefits of systemless root are several. It is easier to unroot (just a factory reset will unroot your device), easier to apply OTA (over-the-air) updates (just re-flash stock boot image to apply OTA update) and it will not soft brick your device, which is a frequent outcome of rooting.
Now, to fix apps do not recognize issue with Systemless Root, you only need to just issue the below commands one-by-one. However, you should first install a Terminal Emulator app from Play Store to issue the commands.
How to Fix Apps Don’t Recognize Systemless Root on Marshmallow Devices
2. Open terminal app and issue the command:
su (if asked, grant SuperSU permission to access the app)
3. Now, issue the below commands one-by one:
mount -o remount,rw /system
mount -o remount,ro /system
4. The last command will reboot your phone.
Now, try an app that did not recognize root access previously. It should recognize and work fine (Source)