Depending on timing, it's quite likely that when you stick in a CD with an autorun script you get: "Do you want to autorun" dialog on bottom Nautilus window for CD on top I don't have a good idea about how to fix this other than maybe sleep(5) && gdk_window_raise(dialog). THe right behavior is perhaps that the nautilus window doesn't open until you click No in the dialog. But I don't have a clue about how to implement that, at least without reintroducing magicdev <=> nautilus IPC.
This is not an issue anymore, as auto-opening new windows has been removed from Nautilus, and magicdev upstream. See the dup. *** This bug has been marked as a duplicate of 106192 ***
Changed to 'CLOSED' state since 'RESOLVED' has been deprecated.