You're correct Jens those links don't have directly anything to do with the problem we were facing. I wasn't sure if I should have posted them but they were the clues we needed to find a temporary workaround to the problem.
This would be great to find a solution in CBL if possible. Unfortunately I don't have an easy way to reproduce the problem although I can describe our setup.
Initially when we encountered this problem we were using CBL to talk directly to CouchDB. Our certificate is from GoDaddy and they use an intermediate certificate to sign our certificate. CouchDB unfortunately doesn't yet support these chained certificates. In order to handle the certificate chaining properly we have a Nginx proxy in front of CouchDB. Nginx handles the certificate chaining fine as we have no problems communicating to our CouchDB server in a browser or terminal.
Let me know if any other information would be helpful. Thanks for your help as always Jens.