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If you are using RepG 40 and have the correct Machine Type selected (one who's driver is "makerbot4gsailfish" as seen in Machine > Machine Information in RepG), then when you "Build to file", the file window which shows up gives you a choice of two output formats: .s3g and .x3g.  You want .x3g (since you're using RepG 40).

Note that the file must be in the top level directory on the SD card.  Subdirectories are not supported.  And the SD card MUST be formatted as FAT16.  (If it's >2GB, your operating system will likely try to format it as something other than FAT16.)