Issues installing new SSL certificate

Hello, I am running ADSelfService Plus build 5304 on Windows 2008R2 and can't seem to get the SSL certificate installed properly.

I used the SSL certification tool to generate a new CSR. I submit the CSR to get an Incommon certificate along with the Incommon Intermediate certificate and add the certificates to the ./jre/bin/SelfService.keystore using the import commands for Verisign certificates. Then I copy the newly created keystore file to the ./conf folder, check the server.xml file and restart ADSelfService plus service.

However I still get a not trusted error and checking the certificate, it shows the certificate is issued by my server instead of the InCommon CA. It's as if the intermmediate certificate is not being properly imported, but I don't believe I receive and error when I import this into the keystore.

Do I need to place the actual host and intermmediate certificates in a specific location?