Hi DanielR79,
Is your Lync server a Standard Edition or an Enterprise Edition?
If it is a Standard Edition, the URL of internal web service should be consistent with FQDN.
If it is an Enterprise Edition, when change the URL of internal web service, you should create another DNS record to it.
Please check if the SIP traffic and HTTP traffic are unblocked.
Here is blog about the process of Lync 2010 client to request the certificate may help you:
http://blogs.technet.com/b/nexthop/archive/2012/11/28/lync-2010-client-authentication.aspx
Best Regards,
Eason Huang


