In addition to adding an intermediate certificate to the certificate chain, you may want to check to see if the correct root certificate is installed on your local truststore, especially if the CA that issued the primary certificate is an internal CA.
The intermediate is important because it ties the root cert (stored on the client machine) to the primary cert (being served from HipChat Server) and establishes the chain of trust.
If you still have issues with SSL installation, please reach out to HipChat support and we can help out: support.atlassian.com
HipChat Server Support Engineer | Atlassian
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