I too have seen this issue. But most of them with Windows. Never had the issue with Windows 2008/2012. But..... the issue is not consistent. With Windows 7 the shutdown does not occur if the Windows 7 VM had been running for quite long time without any restart. Even if i shutdown manually from console, it takes long time to shutdown, occationally just freezes. Same Windows 7 VM if i initiate shut down from Proxmox GUI shutdown button after running just for half an hour or so, it shuts down just fine. I always thought it is because of whatever was Windows 7 doing causing this time out error and nothing has to do with Proxmox itself. Only two or three times i saw the error with Linux VM. Again, they were somewhat loaded and had been running for over 4 months without any reboot.