Go to Start -> Run -> and type in RegEdit
Navigate to: HKEY_LOCAL_MACHINE\SOFTWARE\Square Soft, Inc\FINAL FANTASY VIII\1.00
The DataDrive field value will be the value of your CD burner drive. Change this value to the CD rom drive letter you wish to use.
Note: Everytime you run FF8 Config this value will change back to your first CD rom drive in alph order.
That should do it. Hope that helps.