From #1706064: Compile the Injection Container to disk we changed some code in file_scan_directory() that prevents errors when directories are unreadable, but exist. The change is in http://drupalcode.org/project/drupal.git/blobdiff/408b1cf05ffad1745808b31a9c138fe4efa4eb70..afc4b899455ce0683591de7bd58581e9df5c2e41:/core/includes/file.inc and I was having this issue on a D7 install when doing something like file_scan_directory('/var') which isn't recommended, but shouldn't fail so ungracefully.
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