org-agenda-files skips two files

[Eric Abrahamsen <eric@ericabrahamsen.net>]

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)

Those two files are never in there. I've tried to find at what point in
the code org-agenda-files is first populated: obviously it happens after
org-agenda is called for the first time, but I still can't find it!

All variables related to filtering org agenda files are set to defaults.
I can't see anything about the files themselves that would be
"objectionable". If I open them both manually, the second is added to
the files list, but the first isn't!

Very confused...

Eric