"Operations are in progress, please wait" on Windows 2008/R2 shutdown or restart

We have had for sometime problems when rebooting certain Windows 2008/R2 Servers, they are scheduled for a reboot and then overnight this error is displayed on the console when the server tries to shutdown.  This message is a Windows System Message that is designed to inform you that a task is waiting completion and Windows will not shutdown until it is complete.  This is by design and to avoid data corruption by the shutdown process.

This is outlined in this KB from Acronis http://bit.ly/s5jUba

However there is a problem with this, one is that if you want the server to reboot at 4am and be ready for people the next day and Acronis for example takes until 7am to complete its task, then what is the first thing it does at 7:01am.  It reboots.  Now this is outside your window for a reboot and you get unexpected results and upset users.

Secondly, if the server is a Terminal Server or Remote Desktop Server, then the shutdown process starting stops access to the server via RDP, therefore blocking all your users until the task is complete.

So ultimately this function stops data corruption in your backup but just about renders the server redundant until you discover it is in this state.  If you use MSP tools like GFI RM as we do this will not show as offline as the client can communicate using HTTPS, LogMeIn also shows online for the same reason so it is quite hard to spot until your customer calls you up!

I appreciate the sentiment Acronis but you know what, it would be better to cancel the backup due to the shutdown than to leave a server in this position, because you cannot access the console to stop the process or interact with it you have no choice but to get iLO out or LogMeIn and hard reset, which naturally risks data more than the original backup being cancelled would have.