First of all, thanks for taking the time to post. I am sorry to hear you are having issues with your certificate setup.
That is indeed a most interesting symptom and one I confess I have never been confronted to. The first thing I would recommend doing is to ensure that the address for which the certificates have been issued exactly matches your email address. Indeed, a discrepancy would prevent the process from taking place normally.
Also, just "for kicks", so to speak, you may want to momentarily move your login keychain out of your Keychain folder, then use Keychain First Aid to recreate a fresh one and try again. Should it solve your issue, chances are it was corrupted in a way that wasn't detectable at first sight (it happens). Should it not, just quit Keychain Access, delete the fresh Login keychain, replace it by your old one again and run Keychain First Aid one last time to smooth things back.