Hi Emanuele,
This is really strange. A (resizable) tool window can be resized from any of its four borders and corners, so if you can see the tool's title bar, then you should have no problems to move and resize it as you want. On the other hand, tool windows automatically reposition themselves to stay within screen boundaries, unless your screen's resolution is very low.
As a last resort, you can perform a total reset of PixInsight settings using the Ctrl backdoor:
- If you have PixInsight running, close it.
- Right-click the PixInsight application icon on Finder.
- Press Ctrl and keep it pressed while you select Open from the context menu.
- Say yes when a dialog asks you if you really want to reset all PixInsight settings.
This will leave your PI installation with all factory-default settings.