Use MacOS.OutputSeen() on menuselections: it treats a menu selection in the same way as input to stdin (i.e. as an ack of the output that went before). This makes the CGI tools work nicely for Quit.
diff --git a/Mac/Lib/lib-toolbox/MiniAEFrame.py b/Mac/Lib/lib-toolbox/MiniAEFrame.py
index 31e68b6..87726e9 100644
--- a/Mac/Lib/lib-toolbox/MiniAEFrame.py
+++ b/Mac/Lib/lib-toolbox/MiniAEFrame.py
@@ -81,6 +81,7 @@
 				if c == '.':
 					raise KeyboardInterrupt, "Command-period"
 				if c == 'q':
+					MacOS.OutputSeen()
 					self.quitting = 1
 					return
 		elif what == mouseDown:
@@ -96,6 +97,7 @@
 						name = self.applemenu.GetMenuItemText(item)
 						Menu.OpenDeskAcc(name)
 				elif id == self.quitid and item == 1:
+					MacOS.OutputSeen()
 					self.quitting = 1
 				Menu.HiliteMenu(0)
 				return