I have EXACTLY the same problem. Drupal 7, Dreamhost VPS server, installing WYSIWYG using ckeditor and finder in the library directory tree.
ckfinder works fine, permissions are set in ckfinder-bridge ( https://drupal.org/project/WYSIWYG-CKFinder )
EXCEPT for all downloaded files, they have 411 permissions, access to which is possible after the apache server after downloading.
If I fix the permissions manually (via ssh), then the downloaded file can be downloaded, so this is just a problem with the permissions set at boot time, and permissions in the ckfinder configuration are ignored.
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