Well, I couldn't get the flasher-3.5 working under Windows 7, so I downloaded Ubuntu (a linux distribution which can be booted from CD-ROM without installing) and tried it there. But that shouldn't make any difference if you see the flasher program flash it, and saying the flash was succesfull.

I first flashed the RX-51_2009SE_1.2009.42-11_PR_COMBINED_MR0_ARM.bin rom, which is the global release, because I have a dutch N900. I saw you tried the middle east/northern africa rom, so I assume you live in the middle east or northern africa.

And I used exactly the same command as you did:
flasher-3.5 -F RX-51_2009SE_1.2009.42-11_PR_COMBINED_MR0_ARM.bin -f -R

But that didn't work. So then I flashed it again with the eMMC rom:
flasher-3.5 -F RX-51_2009SE_1.2009.41-1.VANILLA_PR_EMMC_MR0_ARM.bin -f -R

Both times the flasher-3.5 program said something like "flash succesfull" and after this the device worked perfectly except the for microphone. But that is another problem, and has nothing to do with the memory being corrupted.