What imaging tool are you using? LANDesk, ghost, etc...
When the machine reboots you say it's hanging at waiting for command. Is it booting off the network on reboot instead of the local drive?
I am using the Landesk Imaging tool. I am only having this issue on this image technically it is image according to what I see. There is activity on the hard drive during the session. It's supose to boot to the local drive after reboot. If I manually boot the local drive i get the old Non System disk. I have about 30 images that I deploy, they all work fine.