The solution is to open the BizTalk map with an XML editor and change the (GenerateDefaultFixedNodes="Yes") to (GenerateDefaultFixedNodes="No") or (GenerateDefaultFixedNodes="RequiredDefaults"). If you have defaults in your map then you would need to take the last "RequiredDefaults" as you otherwise will miss those in your output.
Remember to test your mappings after you have done this change. See here for more information: http://msdn.microsoft.com/en-us/library/aa561485.aspx
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