So I think I found a way around this issue. Use Feedburner! 🙂 It will actually hide the feeds that you want to hide. 🙂
I’m having the same issue. I’ve tried to add code to the feeds-xxx.php files and google reader is still showing them. However, if I go straight to the feed on http://www.site.com/feed they don’t show up. I’m at a loss as to what exactly is going on.
Hopefully, someone knows but by the looks of this thread I’m not going to get my hopes up.
I had this problem and I added the following line to my .htaccess file on the first line.
Options +FollowSymLinks
poof it’s all working now 🙂