This can occur if IIS holds a hard-coded file lock that causes a 'pending deletion'. The NTFS system is waiting for all handles to the file to close before updating the index, which frees the file.
This situation has been know to happen if you upload a file to your website and then immediately view it with your web browser. When you try and delete the file (or overwrite it), your FTP software throws the "Access denied" error.
If this happens, wait a few minutes and try modifying or deleting the file again.
If the problem is persistent, contact our Technical Support.