As I mentioned earlier, the iPhone can be a rather picky device when it comes to getting it working with Exchange. The following is a list of common issues that prevent the iPhone from being able to reliably access or sync Exchange accounts. This isn't a complete list of all known problems, but being aware of the most likely problems and their causes should help ensure a smoother iPhone implementation.
One potential cause for problems with iPhone/Exchange access is certificate management and SSL. As noted earlier, the iPhone prefers SSL and will attempt to connect to Exchange using SSL during setup as well as when sending ping requests. Microsoft suggests using SSL for all mobile devices with Exchange (which relies largely on HTTP/HTTPs as a communications protocol) because it ensures that casual sniffing of packets will not easily identify ping or sync requests for Exchange.
If you are using SSL, however, it is important that the certificate being used to sign communications is either installed on the iPhone or is signed by a certificate authority trusted by the iPhone. If a certificate cannot be verified, users will receive alerts to that affect when attempting to configure access to an Exchange account and when accessing the account. The inability to verify a certificate may also lead to additional connection and sync problems. Although disabling the use of SSL might appear to be one solution, it raises serious security concerns, particularly if users are connecting via unsecured Wi-Fi networks (which there is no feasible way to prevent).
Internal and external DNS
One of the challenges that the iPhone presents is that it can connect to network resources using a variety of mechanisms: a carrier's mobile network, a Wi-Fi network within your organization, or external Wi-Fi hot spots or home networks. Depending on how DNS and namespaces are implemented in your network, DNS lookups for the name of your Exchange server(s) may return different IP addresses when iPhone users are connected to an internal Wi-Fi network and when they attempt to connect from external Wi-Fi networks or via a carrier's mobile network. (This doesn't typically present a problem for mobile devices that rely solely on a carrier's network, since they will rely on external DNS servers for lookups and thus always receive IP addresses.)
This can result in situations where users can interact with Exchange while at work but not at other times. To avoid this problem, you can either use a VPN configuration on the iPhone or ensure that the DNS records accessed from the iPhone routinely receive an external IP address for your Exchange server(s).This may require review of your Exchange configuration as well as your overall network planning and perimeter devices (firewalls, ISA servers, etc.).