After executing it no need to reboot. Install FlashgordonBB, unselect it's safemode, install SuperSU-v1.99.zip with it, reboot with the phone (not through Flashgordon) ... and enjoy.
I’m curious, is there any reason/benefit to using this Flash Gordon app to install the SuperSU zip as opposed to just using the steps provided by CeBits on the root guide:
How to get the latest SuperSU to avoid the update prompt
First uninstall the SuperSU downloaded from the PlayStore.
1. Visit Chainfire's SuperSU threat here on XDA
2. Scroll down and find the "CWM / TWRP / MobileODIN installable ZIP" download link
3. Download the file and extract it to your phone/PC
4. Once extracted, you will find the latest "superuser.apk" inside the "Common" direcroty
5. Transfer and install the APK file on your phone
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