From mboxrd@z Thu Jan  1 00:00:00 1970
From: Memnon Anon <gegendosenfleisch@googlemail.com>
Subject: Re: org-agenda-files skips two files
Date: Sun, 17 Feb 2013 15:42:59 +0000 (UTC)
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References: <87lianbj45.fsf@ericabrahamsen.net>
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Hi,

Eric Abrahamsen <eric@ericabrahamsen.net> writes:

> I've noticed for a while that two org files in my ~/org directory never
> get added to org-agenda-files, and I can't figure out why. My
> org-agenda-files is set to '("~/org/"), and yet:
>
> (dolist (f (directory-files "~/org" t "org$"))
>   (unless (member f org-agenda-files)
>     (insert (format "%s: %s\n" f (file-attributes f)))))
>
> /home/eric/org/epubnotes.org: (nil 1 1000 100 (20752 42274) (20740 56906) (20740 56906) 10673 -rw-r--r-- nil 8655230 2052)
> /home/eric/org/running.org: (nil 1 1000 100 (20768 26205) (20768 21290) (20768 24128) 423435 -rw-r--r-- nil 5375520 2052)

Did you try edebuging defun org-agenda-files in org.el?

Seems like the relevant bit that extracts all org files from the
directory is:

(apply 'append (mapcar (lambda (f)
			 (if (file-directory-p f)
			     (directory-files
			      f t org-agenda-file-regexp)
			   (list f)))
		       org-agenda-files))

Are epubnotes.org and running.org getting returned with the other files?
Do you have org-agenda-skip-unavailable-files set to t?

Memnon