There are several reasons why cd's may or may not be bootable, here's one possible reason:
IDE vs. SCSI:
IDE is a simple and easy format. There are not many ways to do IDE so it is easy to build a CD that is bootable on IDE. For SCSI, there are so many different SCSI cards (and drivers) that they won't all fit on a bootable image (usually limited to about 1.44M - even on CD). What this means is this: if you want to make a CD that is bootable on a SCSI CD-ROM drive, you first need to know which SCSI controller will control that. You then grab that driver and then you can make a bootable CD for that SCSI controller. The reason that Compaq SmartStart CD's are bootable on Compaq SCSI CD-ROM drives used on Compaq SCSI Controllers is that Compaq has only a couple of SCSI drivers and puts them both on the bootable image and they are done. Compaq SmartStart CD is not likely at all to be bootable on a SCSI CD-ROM drive plugged into a NON-Compaq SCSI controller.
Here's another possible reason from M$: Q155020
If you have any corrections or additions, please contact me.