I am currently setting up my site. I have a number of categories with one being "General." "General" had not been showing up as an option when editing or writing a post. As "General" was noted as the DEFAULT category in the configuration, I thought this might have been the issue. I went to Options, Writing and changed the default post/bookmark to another category which was a parent category of about 15 child categories (and would not be used to post to on my site). When I went back to the Write/Edit post screens, all 15 categories and the parent category were now not showing up. I then changed the default back to General and the categories still were no longer showing in the Write/Edit post screens even though they are all fine in the "Manage Categories" database. I am at a loss to why this happened. No plugins were added during this process so it really shouldn't be a non-core WordPress issue.
I am still in the design phase, so I can delete all categories and start over. This just makes me nervous to ever make a change once the site is live.