The two domains, and in particular the forums, look far too similar -- it's no wonder people get confused. I know they want to keep the same brand identity across both sites, but it would make things a lot easier if, say, .com used light blue instead of grey, or a different font.
Bear in mind that not all self-hosting users will have been to wordpress.org to download the software; many will have used their host's autoinstall feature and assume that wordpress.com is the main site. There should, therefore, be a link to .org from the .com index page and a prominent tagline explaining that these forums are for FREE blogs HOSTED on WORDPRESS.COM only (caps optional ;) )