Symptom: When installing the Monitoring Agent for Lync 2010, I was receiving the following information in the "log" file:

> Deploying Monitoring Server Reports... This might take a few minutes.
The Monitoring Server is using SQL instance "myserver.mydomain".
The data source is using SQL instance "(local)".
The following URL will be used for deployment: https://myserver.mydomain:443/ReportServer
SQL Server logon credentials for "mydomain\myuser" already exist. Use the existing logon credentials.
"[QoEMetrics]" role "[ReportsReadOnlyRole]" has already assigned to "mydomain\myuser".
"[LcsCDR]" role "[ReportsReadOnlyRole]" has already assigned to "mydomain\myuser".
Start to deploy reports...
The underlying connection was closed: Could not establish trust relationship for the SSL/TLS secure channel.
An error occurred when deploying Monitoring Server Reports. For details, see the log.

Turns out this was because I had accidentally forgot to add in the common name to my SSL certificate as a SAN address.  Bottom line, the issue is that your SSL certificate is bad.

Solution:

1. Request a new SSL certificate
   1. Start->mmc
   2. Add in the Certificates snap-in
   3. Select Local Computer
   4. Expand Certificates->Personal->Certificates
   5. Right click, All Tasks->Request new Certificate...
   6. Next
   7. Next
   8. Select your policy
   9. Enter in the information you would like.  Note, if you are adding a SAN address for the short name, make sure you add both the FQDN and the short name as DNS entries in the Alternative name box.
   10. Click on the Private Key tab, expand the little arrow and check Make private key exportable
   11. Click OK
   12. Click Enroll
2. Click Start->All Programs->Microsoft SQL Server 2008 R2->Configuration Tools->Reporting Services Configuration Manager.
3. Click Connect
4. Click Web Service URL
5. Under SSL Certificate, select the appropriate certificate and click Apply
6. At this point, you either saw a bunch of green check marks and you are good to go, or else you probably hit the dreaded "rouge SSL cert" error.  To fix that, please see this link: http://jackstromberg.com/2013/01/sql-server-2008-r2-reporting-services-configuration-manager-create-certificate-binding-failed-hresult-0x80040238/