Is the Unlinking of First Level Parent Items still available in 3.5.3?

Hi,

I have been upgrading to the latest versions of Atahualpa over the last few months. I gratefully used JuggleDad's fix on 3.5.1 to correct the padding and highlighting on my page menus. Then when 3.5.3 came out, incorporating the use of the new WP3 custom menus, I was happy to set up my Page menu in the recommended way, in the position of Menu 1.

The problem is that I no longer seem to be able to unlink first level parent items in that Pages menu. I understand that the relevant option in the Atahualpa Theme Options section is overridden by my using of the WP3 Menus tool, but is there really no way for me to now unlink those first level items.

The site in question is: http://www.apecampaign.org
The menus in question are About, Sign Up, Apes, Threats and Resources.

I've read through other forum threads that touch on this subject, but they seem to suggest that it has been solved (e.g. http://forum.bytesforall.com/showthread.php?t=8079). Am I missing something very obvious?

Thank you in advance...
Eoghan