Creating a UNC Alias for a Windows 2003 Server
There are many reasons my you make want to make a CNAME/alias for a Windows 2003 File Server. These might include ensuring old shortcuts work after a server migration, you might have an application with UNC paths embedded that are very difficult, or impossible to change.
The Problem
Assuming that you have your DNS CNAME created properly, when you try to open the UNC with you'll be asked to Authenticate, (which shouldn't happen)
And even when you try to login, it doesn't work.
The Fix
In order to allow a Windows File sever respond to a alias you need to disable some security by way of editing the registry. These keys need to be created (or editted):
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\lanmanserver\parameters]
"DisableStrictNameChecking"=DWORD:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Lsa]
"DisableLoopbackCheck"=DWORD:00000001
More Information
Here are the links to the offical KB articles.