You will have pressed the button at some point.
The installer does not write those keys, only wbconfig will at the 'you need to reboot screen' when you press the 3rd button.
On the 'WB needs a reboot' dialog there is a 3rd button which will appear the 2nd time this screen shows up. This allows you to set WB to use an alternative method of starting.
It sounds like you have pressed this at some point. If your PC is working without it running then thats ok.