From what I know, if the NTFS system is damaged, then the boot CD won't offer the option of a repair.
In future, get another hard disc, boot up using Knoppix live CD, and use the dd (disc duplicate) facility in the console to make either a binary or file copy of your NTFS partition, and then mess around with the partition. This is how I rescued a broken NTFS system.
I installed a Linux partition and then XP wouldn't boot - just showed smiley face binary garbage. Fixboot and fixmbr didn't work. I made a binary copy of the NTFS partition, reformatted the partition, and then copied the binary image back onto the new partition using dd and Knoppix, and I was back in business. Things were exactly the way they were before.
Other free resources are available e.g. Ultimate boot CD to fix broken Windows systems. If you PM me, I'll mail you a copy of the Knoppix live Linux CD. Knoppix rocks.