Advanced Editor formatting issues

sams0knite

I am not sure if this is something I'm just stuck with, but I enabled the additional features for the Advanced Editor. Everything seemed to be going smoothly, until I noticed that alignment is set to the entire document, and cannot be partitioned. Another thing I've noticed is that the colour resets per line, too.

How would one such as myself resolve this issue, assuming there are any practical fixes? On another note, I have limited PHP experience, so insight is appreciated as well.