The info here; http://codex.wordpress.org/Using_Permalinks
helped me around a few permalink questions quite well.
I can't give you a technical explanation as to why this is, (simply because I don't know), however I can tell you that while using a custom permalink structure such as: /%category%/%postname%/, this problem does not happen to me. (version 2.3.1). The link appears as you would expect, but without the dates, of course. Have you attempted to manually edit the post slug on an affected post title?
Nice site, by the way. I found the contrasts pleasant and the content easy to read. In fact your version made me throw my hacked version of "Mistylook" in the trash bin. :-)