I have a single ISA 2006 server and a Exchange 2003 Front End server both with a Digicert Root Cert, Intermediate certificate and private key certificate installed.
However when verifying my certificate chain - I got errors about the Intermediate certificate not being installed even though it was!
My mobile devices using active sync or Outlook Mobile Access were not connecting... either was Outlook Anywhere.
To fix this I had to delete the root certificate of both the ISA 2006 and Exchange 2003 front end server "DigiCert High Assurance EV Root CA"
Normally you need the Root CA Certificates however ISA 2006 does some weird caching with certificates. Whenever you have ISA 2006 in play you need to delete the root certificates.
Make sure you reboot the ISA 2006 server after it is rebooted. The Exchange 2003 front end server does not need rebooting.