I had that same problem until just now. I found that it could be circumvented by reloading (with F5 or my browser’s reload button) after the initial submission, but it was still somewhat of a bother. Then the article gets submitted properly, so it’s file permissions were not to blame. This occured every time I had posted articles since at least WP 3.1, but the workaround was so easy I had been going with it since.
Today I found that it was due to the wping.fm plugin, so if you’re using that deactivate it and replace it with another ping utility. As usual with WordPress plugins are the first things you should suspect when experiencing errors.