When I run
C:\Program Files (x86)\Microsoft BizTalk Server 2013 R2\XSD_Schema\EDI\MicrosoftEdiXSDTemplates.exe
It asks for the path where to put the files. I accept the default of
C:\Program Files (x86)\Microsoft BizTalk Server 2013 R2\XSD_Schema\EDI\
It appears to run successfully but I don't see any files so I try to run it again. This time it says that the files already exist!
???
My workaround was to expand elsewhere and then copy it to the target location. It said I needed Administrator privileges so I gave them and it worked.