Not all the certificates can be installed as the intermediate or root (they are limited by their "Basic Constraints" which you can see in the View Certificate window on a Details tab).
Sounds to me like a certificate itself is good, but isn't trusted for one of the below reasons:
1. It was signed by the certificate authority that is not trusted, or a chain of trust is broken by some of the certificate that is not trusted
2. A root authority certificate or one of a intermediate certificates is not installed in your browser's certificate store
3. One of your certificates in a chain of trust has expired
4. One of your certificates in a chain of trust is on the black list (CRL)
Take the look at a Certification Path tab and ensure that all of your certificates are OK. If they are bad they should have the red X. Also, you can click on the each node in a certification path to view your certificate at each level; visually inspect your each one and ensure they are completely OK.