I'm having this problem with MULTIPLE installs of 3.3.2, and with MULTIPLE actions, including uploading a ZIPped theme and importing an archive from another WP blog (also running 3.3.2).
And yes, the permissions are correct, or even TOO open (777'd) on whatever folders and files I could find related to each issue, such as the folders and sub-folders for "wp-content". "File.php" also has full permissions.
I've been using WP for a couple years now, many dozen sites, and this just started happeneing all over the place.
--- Example ---
Warning: copy(/home/tonys/public_html/wp/wp-content/uploads/Tonys.zip) [function.copy]: failed to open stream: Permission denied in /home/tonys/public_html/wp/wp-admin/includes/file.php on line 348