I tested on lastest 3.13.0-rc2, the same issue. Use config-3.12-trunk-amd64 as .config, then do make olddefconfig. I also tested on 3.12.2, the same issue. Use working well kernel config-3.11-2-amd64 as .config, then do make olddefconfig. It seems some changes of new kernel break the shutdown function on my machine.