You probalby installed grub into the internal drive. During normal installs grub installs where ever it wants (usually main boot drive). If you want to specify drive, there was an advanced button on screen 8 that gives you a choice of where to install.
If booted into your USB you can easily reinstall from that, or you can use a liveCD.
This reinstalls grub into the drive specified to boot from the install (partition) you run it from:
reinstall from working system - first find Ubuntu drive:
sudo fdisk -l
if it's "/dev/sdb" then just run:
sudo grub-install /dev/sdb
If that returns any errors run:
sudo grub-install --recheck /dev/sdb
Then:
sudo update-grub
Depending on what boot loader you were using on you internal you will have to use a liveCD or windows CD to reinstall that boot loader:
How to restore the Ubuntu/XP/Vista/7 bootloader (Updated for Ubuntu 9.10)
http://ubuntuforums.org/showthread.php?t=1014708
If it is windows you can install a basic boot loader to sda from Ubuntu:
Restore basic windows boot loader
sudo apt-get install lilo
sudo lilo -M /dev/sda mbr
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