Upgrading through FTP can be a big project. Normally one is better off to follow the rebuild vs upgrade method.
The fact that you are not seeing the problem with a rebuild tells me you probably have a file left over from the previous admin profile that is automatically trying to install the old version when you open your admin.
Don't have a copy of the old profiles mod or a spot to check it right now, but did you run the uninstall provided with the mod? It mainly addresses the database
Code:
# @package Admin Profiles# @copyright Copyright 2006-2010 Kuroi Web Design
# @copyright Portions Copyright 2003 Zen Cart Team
# @license http://www.zen-cart.com/license/2_0.txt GNU Public License V2.0
# @version $Id: uninstall_admin_profiles.sql 357 2010-05-23 18:50:07Z kuroi $
DROP TABLE IF EXISTS admin_menu_headers;
DROP TABLE IF EXISTS admin_visible_headers;
DROP TABLE IF EXISTS admin_files;
DROP TABLE IF EXISTS admin_allowed_pages;
Are there still some files left over from the mod? If they are, either replace them with original ZC files or delete them if they were added by the mod.
Lastly, are you getting any debug files you haven't mentioned?
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