I upgraded to WordPress 3.0 awhile back on the site where the below issue was noticed and in fact am running WordPress 3.1 on the site now. Today when attempting to block a new page from showing in the navigation bar via the Mandigo theme Theme Options screen I received an error complaining about permissions. I had to check to see if I had modified anything recently that could have effected these permissions but was unable to come up with anything. Turns out in the changelog that I keep the item that made the most sense was the upgrades from WordPress 2.X to WordPress 3.X. Below I describe the error in more detail followed by how to resolve the issue.
A WordPress site I recently helped develop had an issue related to the header navigation. From a previous request certain pages had been excluded from the header navigation which can be completed in the Mandigo Theme Options section. In Mandigo you can simply check any page to exclude it from the header navigation. Typically if you want to simply add it back to the navigation you remove the check and the page will show in the header navigation in the order in which you have configured it to display using the Order Attribute. In this particular case when I attempted to remove the check and then click the Mandigo Update Options button it appeared to be successful but then the check would still exist in check box I had just removed it from. Below I describe the issue, how I realized what the conflict was, and how to resolve the problem.
One of my favorite themes for WordPress is the Mandigo theme provided by a great developer named Tom from OneHertz.com. The theme is highly customizable and provides ways to customize things outside of the core files so when you upgrade you are not required to make all the modifications over again. I suggest anyone looking for a 2 or 3 column WordPress theme to check this out. One thing I like to do after installing the Mandigo theme is to modify the order of the header navigation. The header navigation links are dynamically generated from top level pages you have created. Below are brief instructions on how to make sure the order of the header navigation menu is in the order you want them to be in as well as a brief description of the code that allows this to happen.
In an attempt to promote as much community as possible I would suggest removing the Website field for when people post comments to your WordPress blog. In this scenario below the Mandingo Theme is being used however it is just as easy to remove the Website field from the default field as well. If people still want to post their web site when making a comment they can do so in the body of the comment.
If you are using the Mandingo Theme then you will need to modify two files but if using the default WordPress Theme you should only need to modify one file. The lines to remove should be the same or very similar no matter what Theme you are using.
In Mandingo follow the below directions to remove the Website field from the comments form when people are not logged in.