Not much I can offer here other than the usual...
1) Is there a file where you THINK there should be? (echo the filename var and then do a FS check)
2) Does the user that the web-server is running as have permission to view/edit/change the file(s) in question? Often YOU'LL have the permission, but user "nobody" or user "web" (typical "users" that the web-server runs as) does not.
THIS APPLIES TO PARENT DIRECTORIES AS WELL!... if permission is granted to /home/you/some_dir/docs for "web", but /home/you is NOT open to "web", then user "web" still can't see the files you've granted permission to.
Most likely it's one or both of these.
-Ben