Would it be something as simple as the localisation?
One is for North America and the other is International English (marked with a Z in the product code).
If I remember correctly, if you have installed your Mac OS with one, it won't accept the other.
If one of the CDs is a copy, then it might not boot / upgrade anyway. I have yet figured out why some burned CDs boot and some don't.
Is it the medium, the way the original CD was imaged or simply some form of copy protection (or all 3)?