1) Open windows like Project Setting or Global Options
2) Create new project or open some older project
Now you can see that Project Setting or Global Options stays on the screen even
if they are not a part of opened project.

Suggested fix: close windows before opening or creating new project. Valid code
should look like this:

WindowManager wm = TopManager.getDefault().getWindowManager();
Workspace[] ws = wm.getWorkspaces();
for(int i = 0; i < ws.length; i++) {
    ws[i].remove();
}

This code can be executed from any thread, at least I hope...