It is a little late, but when installing the boot loader on a usb installation
then the boot loader must be written to the usb device. To do this you set up
your installation, but on the last step before it is committed to disk you look
for a button near the bottom right that says Advanced. You click on that and
then you get to choose where to install the boot loader.

Now that the damage is done you must go through the process of repairing the
Windows bootloader. To do this you will need to follow these steps:www.neowin.net/.../t292614.htmlIf this isn't enough info Google repair Windows boot loader and you find lots of
info. You will need to bot your Windows CD to do this.

Repairing your bootloader will give you the old bootloader which will
automatically boot Windows and will never boot Linux ( not grub, remember). To
get the usb key to boot you will have to change your BIOS to boot from the usb
key before the HD and even then you will probably have to edit grub manually
because grub names the HDs relatively and you have just changed the BIOS so the
old norm and naming scheme is no longer valid. You can avoid changing the BIOS
if there is a hotkey to press to choose the boot device. There is on most HP
computers for example.

To edit grub follow these instructions:www.linuxforums.org/.../69651-grub-edit.htmlIf the usb key won't work, boot the Live Cd and work from there.