Best Guess? You forgot to configure the messaging script correctly and accidentally commanded the script to reduce the message window to zero lines and zero width.
You need to configure the script by editing the numbers for the default size variables (one of the functions is to change the size of the message windows based on two variable values) and then name those variables to make sure that you'll never use them for anything else.
If you forget to do that and use the configured variables for anything else, and set them to zero with the control variable command, then your screenshot is the result - the tiny white line center bottom is all that remains from your message window.
NEVER ignore any script after placing it in your script editor - you always need to read it for its configuration and make sure that everything is set to the correct numbers.
I've moved this thread to Script Support. Please be sure to post your threads in the correct forum next time. Thank you.
If my guess is wrong, please provide a link to yanfly's page with the script description and post your configuration of the script here.