I'd suggest removing all previous Brawlex core files and downloading the latest stable ones. If you have multiple characters that have issues, the easiest way to fix them is to remake their config files. Post in the help section if you get stuck. Also, it is unlikely that an incorrectly configured Brawlex is the source of the AFL not working.
It's not that I have issues, I have two clones from the latest version of BrawlEx, and my other bunch from 1.2.0.0, and so I have to upgrade everyone instead of downgrading two clones. My clone engine has been successful until I tried adding the alt. stage loader.