When flashing the eMMC content, always flash the FIASCO/Rootfs image and then flash the eMMC. Do not boot up the device between the two i.e do NOT use the -R parameter at the end!
flasher-3.5.exe -F RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin -f -R