How to create certificate authority certificate with makecert?

Maybe you could try adding the -cy authority parameter on the root certificate creation, like that:

makecert -n "CN=root signing authority" -cy authority -r -sv root.pvk root.cer

Thus you declare you are creating an authority certificate and that should do the job.. or at least take you on track =)

I tried myself to create a root certificate using this commandline and to import it into Firefox: I can confirm that if you don't add the "-cy" parameter, Firefox will not consider that a valid root certificate.

Hope that helps!