I’m having a similar if not identical problem.
I created categories and select different ones when writing posts, but WP doesn’t even save those selections. The result is uncategorized posts. Everything worked fine initially, and then it stopped.
see what I mean : http:www//johnros.com/index.php
The .htaccess in my root directory is set to 775.
Could this possibly be a problem with one of the plug-ins? I’ve installed the latest miniblog, wysiwyg, contact and spell checker.