Zackery , the problem lies in that firmwares are hardware sensitive. It is likely that both players have some slight difference in hardware components. An incompatible firmware would render the player dead.
However, if you are adventurous enough, there is a new S1clone v1.3 developed by wiRe that could extract the firmwares off your player. See thread here
http://www.mympxplayer.org/new-s1clone-v13-vt8057.html
i'll suggest that you extract a backup copy of the player that you are going to overwrite first. Just in case the new firmware does not work.