Files uploaded using the HTTP/S client are first created in the temporary files directory for the user account. The file is then moved to the destination directory after the upload is completed. Because the file is created in the temporary files folder, the permissions for that file are inherited from that directory. This can sometimes cause problems for users that log in using Active Directory authentication.
Take a look at the temporary files folder, and try modifying the default permissions for that folder to have the desired permissions to allow all AD users read/write permission. The temp folder would be the temporary files folder associated with the account of the AD user, for AD authenticated users, or the temp folder associated with the service account running Cerberus, for native users.
It could be:
on Windows 2008 R2 for AD users, or
For the Local System account. Many systems are configured so that even the AD users temporary files are created in C:\Windows\Temp.
Cerberus FTP Server 6.0.1 now includes the ability to override the default location where temporary HTTP upload files are created. You can access this setting in the Advanced page of the Server Manager. A reboot of the server is required after changing the temporary HTTP upload folder location.