Thanks for the detailed explanation and the screenshot. The issue occurred because the message window wasn't resetting its coordinates to the default upon closing, causing the choice window (which relies on the message window for positioning) to misalign and appear in the wrong place. I also added an adjustment so the choice window correctly follows the speech bubbles if they are displayed simultaneously.
Could you download the JS file again and test if it's working correctly now?
Thanks for the feedback and all the information.