Apparently; in WordPress there’s a bug that hasn’t been addressed.  Until it’s fixed I’ve hacked my site to ignore it by commenting out several lines of code that display the “catagories” section.  The problem that others are also having is this…as you make categories so you can properly sort your posts they don’t show up!  For the search engines:  WordPress categorizes not showing.  Back to my post, all I saw was, “Home” and “Uncatagorized”.  This was personally irritating and if I want to waste more time maybe I’ll look into it, but I’m not an “expert” which is why I said “I’ve hacked my site”.  I know enough to be dangerous, LOOKOUT!   I don’t think it’s a MySQL problem, hard disk problem, etc as some have posted if you search for it online although they said it fixed it for them.  It might be a permissions problem but I think that’s unlikely.  Permissions on my WordPress folder tree don’t seem to be it in my mind (but I won’t rule it out either).  If you’re an eager beaver and feel like doing the same thing I did this is what I did.  Oh, this is the site I was looking at when I got the brilliant idea to just change how the template works —> Here.

I commented out code to ignore the categories and only post my “pages” as my links, it’ll work for now since the home page shows everything in the “uncategorized” group anyway.  Now – there is one quirk here but it’s less irritating than the former quirk.  The quirk being, the “Home” link doesn’t get you back to the root page if you click your other page links but for me it’s something I can live with, if they want to go back to the root page they can click the top most URL.

In your theme folder (I’m using “pixel”):  /wp-content/themes/pixel

Edit this file and code, it might not look “exactly” like mine but it’ll be close!:  header.php

Original Code that listed the pages in the upper right hand of the page:

div id=”topright“>
<?php wp_list_pages(‘depth=1&title_li=0&sort_column=menu_order’); ?>
<li><a href=”#searchform”>search</a></li>
<li><a href=”#main”>skip to content &darr;</a></li>
</div> <!– Closes header –>

Comment out the PHP with // and leave the rest unless you don’t want it:

<?php // wp_list_pages(‘depth=1&title_li=0&sort_column=menu_order’); ?>

I then edited the code below  to list the pages instead of the categories:

Original Code, not this is NOT the same code we just edited, this code is what should be next in line in your header.php:

<div id=”catnav”>
<div id=”toprss”><a href=”<?php bloginfo(‘rss2_url’); ?>”><img src=”<?php bloginfo(‘template_directory’); ?>/images/rss-trans.png” alt=”<?php bloginfo(‘name’); ?>” width=”65″ height=”24″ /></a></div> <!– Closes toprss –>
<ul id=”nav”>
<li><a href=”<?php echo get_option(‘home’); ?>”>Home</a></li>
<?php wp_list_categories(‘sort_column=name&title_li=&depth=2’); ?>
</div> <!– Closes catnav –>

Edit this line and change to list pages, the part in ITALICS is from the original code listing it “topright”:

<?php wp_list_pages(‘depth=1&title_li=0&sort_column=menu_order’); ?>

Results: Took catagories not showing away all together and replaced them with normal page links but on the homepage the uncatagorized posts still show as default which is still sort of a problem but much better than the original problem.  If you rename your originals and keep them you can easily flip back once the real solution is found!  Keep digging and let me know if you find it, I’ll do the same if I find it.