I've had an SSL certificate installed for my Tomcat web application for the past year, running just fine. As the certificate is expiring, I needed to replace it. I went through the usual channels, generated a new CRT, and got a replacement certificate from GoDaddy (the certificate provider).
I then created a new keystore using my certificate and the root, cross, and intermediate certs provided by GoDaddy. I noted that when the keystore was complete, 3 of the 4 entries were identical to the existing, working keystore on the live site (although the listing order of the cross and intermed certs were reversed; does that matter?). The one entry that was different was my own, new certificate--which makes sense. This was all very encouraging.
Nonetheless, when I installed the new keystore on my webapp's site, I got an Untrusted Certificate Warning from the browser when I tried to access my site. When I called GoDaddy tech support about this, the rep said that it's because I have two outstanding certificates on the same site and that the warning will go away when the old one expires next week. I am highly dubious of this theory, and if it's incorrect, then I will be left the morning of without a properly functioning cert and no ideas on how to fix it.
What could be the real reason behind the Untrusted Cert warning?