No need to respond to the questions that I posted. I was able to duplicate the issue. I was also able to determine what is happening. The AutoOrganize Settings dialog does indeed get displayed in this situation. However, it is showing up behind the main window. You can see this if you press Alt+Space after invoking the dialog. You will see a popup menu show up with Move and Close on it. If you click on the Move menu item, the mouse cursor will change and then you can hold down the left mouse button and drag the dialog window out from behind the main window.
The odd thing is that other than centering the dialogs to the main form, we do not do anything to affect the z-order of the dialog box. This is handled by Delphi. I'm going to do some more testing but right now it appears that keeping dialog boxes in front of stay-on-top forms was broken in Delphi XE2.
For now, you can turn stay-on-top off, otherwise, you can use the Alt+Space trick above to help if you get into that situation.
Thanks for the report.