I think I see the source of your confusion.
In the instructions, #3 says:
Reboot your computer into Safe Mode with Networking
using the instructions for your version of Windows found in the following tutorial:
How to start Windows in Safe Mode
When following the steps in the above tutorial, select Safe Mode with Networking
rather than just Safe Mode. When the computer reboots into Safe Mode with Networking make sure you login with the username you normally use. When you are at your Windows desktop, please continue with the rest of the steps.
Then #13 says:
When the installation begins, keep following the prompts in order to continue with the installation process. Do not make any changes to default settings and when the program has finished installing, make sure you leave both the Update Malwarebytes' Anti-Malware
and Launch Malwarebytes' Anti-Malware
checked. Then click on the Finish
button. If MalwareBytes' prompts you to reboot, please do not
I had misread #13 at first and missed -the now red since I changed it here - 'not'.
So I think the answer to your question your question is yes - run RKill and MBAM in Safe Mode with Networking.
Said as nicely as I can... At the bottom of the self help guide that you referenced, it says:If you have any questions about this self-help guide then please post those questions in our AntiVirus, Firewall and Privacy Products and Protection Methods forum and someone will help you.
Edited by Bill253, 17 February 2011 - 10:28 AM.