It sounds like IIS isn't serving out batch (.bat) files quite right. Normally batch files cannot be "run from source" if the source is an HTTP share, so make sure your delivery method isn't set to run from source. It is also possible that the MIME types were modified to prevent downloading of .bat files from IIS. The command appears to modify the MIME types (which can also be done from IIS Admin tool) to allow .bat files to be downloaded.
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