You could try passing the parent widget to the routine that creates the new Toplevel and then call $parentwidget->focus to give the parent widget focus. You could bind this method to when your new window takes focus.

In Mastering Perl/Tk, there's also the method $widget->focusForce, which allows you to "force a widget to have the focus even if the applicatuion isn't currently active" (p. 299, Mastering Perl/Tk).