I tried, but I didn't manage to replicate this issue. I installed only eli book and message manager. Reseted all the positions settings to default.
Tried with openness align set to none. Tried with the switch on and off. But nothing. The window closes normally and don't stay on the screen.
1 - Make sure you have the latest core scripts updated by going into the Game menu dropdown on the RPG Maker software and click on "Update Core script"
2 - Are you using another plugin that mess with the message? Or battle ui/windows? Because on my tests here, by default, the battle ui is not centered on the bottom of the screen, but instead, it fills the entire game screen horizontally. But on your screenshot it is centered.
3 - If none of the above solved, you need to tell me exactly what you are doing so I can mimic exactly that to replicate the issue: Plugin configurations etc. Otherwise, send me a sample project replicating the issue so I can take a look. Can send a link here or through my discord: hakuenstudio