Could someone please explain what the issue is with state birth certificates?

We received an official looking birth certificate with seal from the hospital where our son was born and have used it to register him as a military dependent and enroll in three different schools (public and private) in two different states.

We tried to use it to register him for SLYSA who rejected the birth certificate. I didn't even know there were different kinds of birth certificates. The fine print on the hospital one revealed that it is indeed not official and that you have to contact the Vital Statistic at the state capital.

A call to the MYSA office revealed that they have been fielding many calls regarding this issue on a daily basis. It seems that the distinction between the different types of birth certificates is not clear to many people. For people born in MO it is a pretty easy issue to resolve but for others it is more difficult. Our son's birth state says the normal mail (won't fax) turn around time is 4 weeks but they are currently backlogged.

It seems that if this is a common problem it should have been more clearly communicated to the families filling out the forms.