Damn, I had no idea, I thought one controlled the other. That would explain the massive problems I was getting with description.ext as I was making the changes there until you guys helped me out.
All I want is to have a custom compiles.sqf
Yes I did. I will correct that and put the PBO's back to their original files. I will then copy what I need into my mission folder and edit from there. Thank you very much guys. I will keep you posted.
It worked, Seaweed and Rosska - you guys are f****** heroes, thank you so much.