Running the boot-repair tool does more than fix grub. It looks like it busted your windows boot config. If you run the "startup repair" program that is on your windows 7 install disk, that should fix your Windows boot, but will probably again overwrite grub.
To fix this, try following the following steps:
Boot from the live CD.
Open up a terminal and find out which partition has your Ubuntu installation:
sudo fdisk -l
Mount your partition:
sudo mount /dev/sdaX /mnt # sdaX is the partition that has Ubuntu
Bind mount some other necessary stuff:
for i in /sys /proc /run /dev; do sudo mount --bind "$i" "/mnt$i"; done
chroot into your Ubuntu install:
sudo chroot /mnt
At this point, you're in your install, not the live CD, and running as root.
If everything worked without errors, then you're all set:
At this point, you should be able to choose which OS you want to boot into on startup.