Hi ShadowChorus,
I'm very sorry for the late reply; I didn't get a notification for your post :(
I don't think this is a problem related to this plugin. A window appears when the eventing tells it to appear, so it's in the game dev's hands after all. I understand that the RPG Maker engine makes it a bit hard to display speech bubbles in sequence without freezing the game.
What you probably want is to use parallel process. Wait events inside events running on parallel processes do not freeze your game.