My brothers girlfriend has this problem with XP Home just a couple days ago. All i did to correct it was boot off the XP cd and run scandisk. She is back to using it with no issues.
I wouldnt blame vista...you should have bought an internal dvd rom drive. Also the upgrade from XP to vista (assuming thats what you did) isnt, in my opinion, the best way to go. Upgrades are horrible from my experiance. They never seem to work right and they never "feel" right either. They always seem to bring extra baggage from the old OS. A clean installation seems to do the trick. There is a way to use your upgrade cd to do a clean full installation but i cant remember the steps. Google would know
But back to the problem..If the computer wont boot off the cd with the external dvd rom drive then i would go into the bios and see if you can find a boot USB option in your bootup settings. If not then that means your motherboard doesnt support booting from USB devices. The only way to correct that is get an internal DVD drive.