Problem
When trying to sign in to Lync get the following error:
There was a problem verifying the certificate

Solution
It’s either a certificate trust issue or a DNS name mismatch to the certificate that you have issued.  
The PC or device which you are using to logon to Lync needs to trust the certificate chain from which you generated the Lync certificate(s) and the DNS records used to locate and connect to the Lync server need to match the name(s) on the certificate.

In my case I was using Manual Login and pointed to the IP address which was obviously not in the certificate :p