In the process of maintaining some existing maps, I interestingly came across the following error message, whenever I attempted to build the schemas project.
Node <node name> – Specify a valid .NET type name for this root node. The current .NET type name of this root node is a duplicate.
When I opened the offending schema (which contained a number of imports) using the BizTalk mapper in VS.NET, the schema did indeed appear to contain repeating (or duplicate) nodes. After digging a little deeper by manually studying the schemas using a simple text editor (notepad2 in-fact) discovered that the schema definitions were sound. The mapper was misbehaving. After a quick google, soon located an official article (KB922431) and hotfix for this bug. To get the hotfix a request must be submitted to Microsoft Online Customer Services.
More details about the problem and the resolution can be found here.