I've just got myself a Seagate 2TB HDD and my seagate 1TB is nearly full (this is a 2nd drive as I've got a SSD for windows. I got Acronis true image 2014 with the drive, tried the clone option. No go. it reboots to do it's thing and fails straight away saying something about unable to mount recovery. so after trying that several times, I've just copied the entire contents over, but if I remove the 1TB drive leaving the SSD and the 2TB drives the PC wont boot, SSD alone wont boot either. Under Computer management in windows I've got this. So as you can see windows claims the 1TB has "system" on it. Acronis shows this
Your boot manager is on the wrong drive. I would mark the windows partition as active, reboot without the other disks using the windows recovery DVD and give this a try: http://www.howtogeek.com/howto/32523/how-to-manually-repair-windows-7-boot-loader-problems/
Thanks for the reply, I'll give it a go. I was hoping for something else as I don't want to risk having to reinstall everything if something goes wrong.