When you install EPiServer it adds a number of dlls in the GAC, so that's why it works on your local machine and not on the build machine.
The section in the web.config is a custom configuration section (read more about them here (How to: Create Custom Configuration Sections Using ConfigurationSection) defined in the EPiServer.Configuration.dll. You can add that as a reference to your project (setting Copy Local to true), or you can simply install EPiServer on your build machine. I've done the latter, since the build machine then won't choke on any EPiServer dll whether or not you've added them to your project.