There was a critical severity, "highest omg bbq" priority bug in 2.5 related to feed files (Ticket #6460). It was fixed in 2.5.1
I am suffering identical symptoms, even though (and this is the spooky bit), I am running 2.5.1.
(The rest of this post is to help you take me seriously - I want to show to you that I am suffering the same symptoms, and that I haven't made the most common newbie mistakes.)
Under some circumstances, the feeds on my blog are returning that there are no posts or comments. The files are not empty. They have all the standard feed headers - they just have 0 posts or comments.
If you visit the "official" feed URLs (e.g. example.com/blog/feed or example.com/blog/feed/atom) it works perfectly.
If you visit the old-fashioned feed URLs that piint directly to PHP files (e.g. example.com/blog/wp-rss2.php, example.com/blog/wp-commentsrss2.php, example.com/blog/wp-atom.php) it gives empty files. Of course, Bloglines and Feed-Fetcher are looking at these ones, so I need to fix the problem.
My blog is in a subdirectory of my site (note example.com, but example.com/blog). This was one of the preconditions of the #6460 bug.
The problem does not occurs when permalinks are set to default. It does when they are set to Day and name. Changing to Default and back to Day and name doesn't make the problem go away.
#6460 was fixed in 2.5.1 (with Change Set ).
You are probably thinking I am making a newbie mistake, by not running on that version.
Not so: I resynched all the 2.5.1 files across, to be sure. They were already up-to-date.
Here is an example line (799) of my wp-includes/rewrite.php file.
'.*/wp-rss2.php$' => $this->index .'?feed=rss2',
It has the necessary "/" character, that should fix the problem.
You are probably thinking I am making a newbie mistake, by not running upgrading my database.
Not so: I confirmed the database was up to date. Then I hacked version.php and incremented the number by 1, to force another databse upgrade. No change.
You are probably thinking I am making a newbie mistake, by having an incompatible plugin.
Not so: First I reproduced the problem exactly on a test blog. Then I turned off every single plugin. Still no luck.
Any other hints?