The problem is that during Writing a Post, the only categories listed are Blogroll, Uncategorised abd Web Programming. However, my actual categories definied under the Manage section:
So far there is one post that is in the CSS (and therefore Web Programming) category.
There is some tie however to the blogroll link categories. If I have an uncategorized link (i only have one link in my blogroll right now) then it displays all categories in the write post section, but if the blogroll link is under web programming, the only categories available are uncategorized, blogroll, and web programming