Making a script wait for a GUI to stop running before returning?

I have a Jar that contains a swing GUI that I wish to run from a Groovy script, but when I try to make the script wait for the GUI thread in any way, Filemaker and a partially opened window for the Swing app becomes non-responsive and I have to force close it. I am working on OS X, but writing a plugin that will be used on both OS X and Windows.

The Gui ends up possibly saving a file that the script needs to check whether it was made or not to continue. It's a user-choice and if the file isn't saved, the script can end, but if the file is there, the script needs to continue, but I cannot find a way to successfully open the GUI and prevent the script from finishing.

Somethings I have tried are various versions of thread synchronization, causing the script to wait until it is notified by the GUI, as well as just a simple while(gui.isVisible()). All of these result in both the app and filemaker/scriptmaster becoming unresponsive.

It seems to me that there is an issue with multithreading with Groovy and Scriptmaster, but I cannot find a way around this.

Does anyone have any other clues on how this could be done.

Thanks in advance.