This has been happening quite a bit lately:
I open Script Debugger, display Data Viewer, step through a script, stop it when I reach a point in the script that I want to change, and close both the Script Debugger and the Data Viewer windows.
The next time I press a button that runs any script, the Script Debugger window opens. I can close it, but it displays for every script that I run after that. Closing the application window and restarting FMPA appears to be the only way to turn off this behavior.