Recently we moved our server from a Windows 2003 server with Exchange 2003 to a Windows 2008 R2 with Exchange 2010.
I have worked through most of the speed bumps and I got nearly everything working. I moved our SSL cert that we use for Exchange / OWA / OMA following this guide
And this Guide
I bound the Cert to our Site by following this guide
I also went to where we got our Cert which is Comodo and I grabbed what I think where the proper Root and Intermediate Certs judging by the certs on the old server and the cert I exported from the old server.
And about 10 others to make sure I wasn't missing anything. I was able to get all of the cell phones to sync with ActiveSync / OMA and I can access OWA just fine but all of the INTERNAL desktops are getting a Security Alert from Outlook every few hours.
I will attach a screenshot of the error and it does tell me that the error is caused by "The name on the security certificate is invalid or does not match the name of the site" however the exchange site is still Exchange.Company.com. The server name itself is different but everything else if is the same.