Using ATI boot disk causes Windows OS to not startup

I tried making a backup using a ATI Home 2011 boot disk on a new computer set-up running Windows server 2008R2. I thought that if this worked well I would get the server software and install it on the new machine. There are 2 hard drives set up in RAID 1 using the Intel RAID Controller Driver software and configured in the BIOS settings. The boot disk started and both drives showed up, instead of one as I would expect for RAID1. I then quit and tried to boot the computer in Windows but the following error showed up:
"Windows Boot Manager
Windows failed to start. A recent hardware or software change might be the cause. To fix the problem:
1. Insert your windows installation disc and restart your computer.
2. Choose your language settings and click "Next."
3. Click "repair your computer."#

Status: 0xc000000e

Info: The boot selection failed because a required device is inaccessible"

I opened the Windows repair function to get the command screen and tried to rebuild the bcd but it couldn't see the drive that Windows was installed on, and didn't work.

I re-installed Windows thinking maybe Windows was the problem, and tried again, but the same thing happened.

Any ideas as to what using the Acronis boot disk is doing to prevent Windows booting?