The reason that the target of the menu item resolves differently is because of the way that you setup Jooomla SEO.
I'll let you into a little secret. Every time I build a new Joomla website (and I've lost count of the number of times I have done that), the very first thing that I do after I have installed Joomla - before I've done anything else - is that I setup Joomla SEO. The very first thing that I do is go to the Global Configuration and click two radio buttons and then I rename htaccess.txt to .htaccess and then I go to the front page of my website to make sure it's properly working.
If you setup Joomla SEO as the first thing, all the menu links that you create after that will be generated in the right way.
Now, as far as your K 1.6 configuration report is concerned, we have a problem and I will need to discuss it with the Kunena project team. The problem is that the configuration report bases some information on your domain name and not on a folder lying beneath that domain name. If your site "root" (of your test site) is a folder of your domain name then we only see the "parent" domain, not the "subdomain". This problem is easily overcome if you setup your test site folder as a subdomain ... but that's overcomplicating matters on your side. We need to find a way to report the actual root that shows your website. Don't worry if you don't follow what I've just written; I'm thinking aloud so that others in the project team might understand the problem we've got.
In conclusion, most 404 errors occur because of mismanaged SEO and/or improperly targeted menu items.