This is a long post about an issue that seems to have gone away. Odd enough to warrant some record of it IMO, so here it is...
Background - I am setting up a brand new install of WordPress on new server space for a client (http://new.charlestonvolleyball.net). The install from the host was WP 3.4.3 using a cPanel install script. The MySQL DB was created via the script, an admin created, and the initial site started.
Initial Setup - Login as admin. Upgrade to WP3.5. Update Akismet. Install Akismet API key. Switch to Twenty Twelve Theme. Delete other themes (2010/11).
Nothing crazy yet. Change the start page content/permalink. Change the initial Hello World post. Setup some new post categories. All is good. Add some pages, still good.
Add a custom menu and set it as the main (primary) menu. Then all heck breaks loose. The home page now says "Nothing Found" (it is set to recent blog posts).
I change the home page to a static page. I create a new blog category called "blog". I add assign my only post to the new blog category and keep it attached to "general" (the prior category). I then add a new item to the custom menu that links to the blog category "blog" so I can have a quick & easy way to get to the site "blog roll".
Click my new link. "Nothing Found".
I look at Post/Categories. All categories show a post count of 0.
I look at my post. It is assigned to "general, blog". Edit, save. Categories still 0.
I copy the post content. I create a new post. Set the category to only "blog" this time. Save. Yipee, the post appears on my new "Blog" menu link. Categories show 1 for blog. All is good with the world.
I delete the original post that used to be "hello world". Save.
Go back to the blog page. "Nothing found".
Check categories. Counts = 0.
Edit/save the new post. Counts = 0.
Copy content to new post "Test". Assign to "blog" category. Check categories page. Blog count = 1.
I've now changed the title back to "New Website, New Year", assign to the "blog, general" categories, and changed the permalink. blog & general count=1.
I'm not sure what was triggering the disconnect between the post & assigned categories on the first 2 attempts, but something was going haywire with WordPress 3.5 and Twenty Twelve. Nothing special installed yet outside of enabling Akismet, so no plugins/3rd party themes to blame.
Didn't want to report as a bug since it seems to be OK now, but figured I'd record some details in case this "ghost problem" appears for someone else. Maybe this record will help track it as something more than a 1-time fluke... or maybe I just ran into the 1-time fluke.
For now things seem back to normal so I guess this post can be "resolved".