Okay - now I see what you're doing. Okay, so you have WordPress in the root, and you're faking that it's in another directory. I've actually never done it that way before - probably why I'm not familiar with this setup.
From my understanding, the RSS feed will point to however your permalink structure is set up. You didn't mention if you took this step or not.
If you did, and it's still not working, maybe try using .htaccess to rewrite the URL? I don't know exactly how to do that...and I don't know if that would mess up your current permalink structure (if you already have one).
And example of using .htaccess to change your feed's URL (this one uses feedburner - so you'll have to edit it to suit your needs - but it gives you a starting point):
Options +FollowSymLinks
rewriteEngine on
rewriteCond %{HTTP_USER_AGENT} !feedBurner
rewriteCond %{QUERY_STRING} ^option=com_rss&feed=RSS2.0&no_html=1$
rewriteRule ^index2\.php$ http://feeds.example.com/myfeedname? [R=301,L]
the "^index2.\php" being the current link to the feed, and the stuff from "http://..." on would be the new URL.
You *should* be able to append this into your current .htaccess file - but like I said, I don't know what effect this will have on the rest of the site, and you'll have to play with that a bit to get exactly what you want.
After all of that, I hope it helps!