This is what's behind the "Begin Download" button on Fuji's site "http://download.fujifilm.co.jp/pub/tools/xt1zFdD1N8Z/FWUP0005.DAT"... there's only one file in this link.. For whatever reason interaction between your Mac and the Fuji web site is triggering two consecutive download requests of the same thing. Since the OS won't support two identical filenames in the same download location the second gets renamed.
I'm not questioning the outcome at your end... simply saying this does not happen with Windows 7 and Firefox browser, period. Finally, my point about having multiple firmware files on the same SD card was not about keeping older versions. I keep the latest version of X-E1, X-E2, X-T1 and lens firmwares all on the same SD card in order to update other cameras or lenses from a single card.