|1st of all, you need to double check the boot order setting in the BIOS to make sure your CD drive is listed before the HDD.|
2nd, when you attempt to boot off the Windows CD, you need to "press any key..." when prompted. If you don't, the system will bypass the CD & move on to the HDD. If you're not seeing the prompt, it may be hidden behind the splash screen.
3rd, don't guess that you have a rootkit. Run a program such as "rootkit revealer" to confirm that one is present. If there is, then it's just a matter of determining the best way to remove it. Many times, repairing the MBR will take care of it.