You have yanfly's message system installed and forgot to name and configure the variables for it - that's why now that specific variable has two functions: the one you're using it for, and the one Yanfly's script is using it for.
You cannot simply assume that a script functions without configuration once you placed it into the script manager, you ALWAYS have to check if it uses switches or variables to allow configurations by events, and if yes you have to make sure that those variables are not used for anything else (usually by first setting the variable number in the script to a still unused variable, and then naming that variable something like "yanfly windows size" to prevent yourself from using it for something else after you added the script.
And do not only correct that for Yanfly's message system, check all your scripts for similiar things (some scripts configure through variables 99/100, you'll get similiar problems if you ever get to those numbers without reserving them).