Problem with nav-menus.php on Mystique

Hello,
I’m running WordPress 3.0.4 with theme Mystique 2.4.2 and no plugins.
I have always employed Mystique with Pages as the primary nav, using just Mystique Settings to make that so. Now in a recent upgrade, I needed to employ the custom menus feature.

Now, when I am going to employ custom menus, the Appearance/Menus screen (nav-menus.php) does not show me anything but a grayed out Custom Links box, so I am unable to create a new menu or select which menu to use as primary navigation. Oddly, though, it does work just fine on my local version of my site, this only happens on the live version of it. So, I guess this leads me to think of some MySQL access restriction or something?
Could anyone with better knowledge of the Custom Menus feature perhaps help me figure this out?

Here are my steps:
I made a full copy of the site from the server to my local LAMP (the Linux Apache MySQL PHP bundle) on which to work. So I made several modifications to the theme (adding taxonomy.php, modifying style.css, single.php, core.php to change the appearance of the loop and functions.php to add 3 custom taxonomies). Then, when I implemented the changes, I first deleted the entire original /wp-content/themes/mystique/ directory and then uploaded the new modified directory, without switching out of the theme on wp-admin (not sure if this is the correct way to upgrade a theme).