Check to make sure auto-cert provision is enabled. If not you would have to whitelist the APs before they would be allowed to come up. If the mesh APs have never been cert provisioned, they will come up, pull the cert, reload, and come up again so it WILL take some time, but auto-cert provision should be enabled, or you will need to find those APs and allow them in the whitelist.
As Colin notes though, TAC would be a good next step, we don't do much with 6.4 in the field anymore so I don't know if there's some latent issues. But generally it's not usually an issue.