When you mentioned upgrading was that from an older version of Windows like 9X, ME, or 2000? A full version or recovery disk is a bootable disk while upgrades generally only work while booted into a previous version where you start the installer from there.
You may have simply reinstall the prior version and upgrade from there all over again unless you simpy forgot the reverse of what I mentioned before and never set the first item in the boot order to cd rom. The bios is looking at the hard drive for a boot loader of any OS rather then seeing the disk in the drive.