I've got everything up and running now working well except one thing. I bought a certificate with GoDaddy and tried to install it. I followed the instructions here:

Everything worked fine in the installtion process except I still get a certificate error when I browse my webpage.

I can see that the webpage is using the correct certificate and its active in Filr but the certificate path is missing and the browser says "The server's certificate is not trusted"
I tried to install the intermediate certificate, tried to use keytool to install the certificates, I also tried installing a p7b certificate. I also tried to generate a new request and rekey my certificate but always the same issue. I have set up two Filr servers and Im having the same certificate problem on both of them.