Non-clean to Clean option turned on not working by default

I recently found out through Google webmaster tools that
www.example.com/?q=node/1 got indexed and surely enough they appeared as an url and was not rediected to the url alias.

After enabling the Remove Trailing Zero Argument today in the Global redirect admin Global redirect now correctly redericts to the url alias url.

I have been using Global redirect for quite some time now.