It makes sense, the firmware provided is not correct. The v9.0.31.1487 is a full 1.5MB image and not the update that the FWUpdLcl tool requires. You could always reflash the latest Asus bios which will revert the ME firmware as well.

EDIT: Actually probably I'm mistaken. Does Intel use the full ME 1.5MB firmware nowadays (after 7-series)?

Flash this, extracted from the latest Maximus VI Extreme Bios.

EDIT: The file says IV but it's VI, mistake...

The forum attachments seem to be broken right now, anyway this is a temp link:

http://www.mediafire.com/download/18bwh2...usMaximusVI.rar

I don't have ME v9 experience but are you still using a v9.1 FWUpdLcl tool? Maybe it's not accepting to flash anything but v9.1 firmware. Try this package below with the command

FWUpdLcl64 -f ME_9.0.30.1482.bin -allowsv

If it works, restart. Then you can update to the latest ME 9.0 version with the command

FWUpdLcl64 -f ME_9.0.31.1487.bin -allowsv

Link: http://www.mediafire.com/download/ab18zu....0.31_1.5MB.rar

The only way then is to reflash the whole BIOS using FPT. This will overwrite everything including the "new" ME. Asus is using EFI Capsule files (.cap) which cannot be flashed with FPT directly. You need to use a tool such as FTK by @CodeRush with instructions found here:

http://hardforum.com/showthread.php?t=1726429

EDIT:

Regarding what I said HERE, I think I figured it out:

Up until 6-series (ME7) the FWUpdLcl tool could only use Intel Update .bin files
From 7-series (ME8) and up the FWUpdLcl tool can use both Intel Update .bin files and full ME regions (17D000 for 1.5MB)

I extracted the ME from my 6-series system and tried to check it's version with FWUpdLcl. It didn't show the correct number but it did for the update file.
I extracted the ME from my 7-series system and tried to check it's version with FWUpdLcl. It worked like a charm for both full and update ME firmwares.

What's the difference though? Probably that the full ME also includes the custom motherboard settings like ICC etc. In that case, shouldn't that cause issues on different systems? Can anyone shade some light into that?

These are the instructions by CodeRush as shown at step 5.4 of the guide I linked above:

1. Download and extract the file from the link, it included the DOS version of FTK9 v0.10 + Maximus VI Extreme latest BIOS
2. Make a bootable MSDOS/FreeDOS USB flash drive using Rufus
3. Copy the contents of FTK9_0.10_DOS folder at the root directory of the flash drive
4. Restart and boot via your USB flash drive
5. Type merefl and press enter
6. It should start reflashing your ME firmware
7. When done type poweroff and press enter
8. Remove power from PC for 30 seconds to make sure ME is reset

Link: http://www.mediafire.com/download/n6060w..._DOS_M-VI-E.rar

Source: http://hardforum.com/showthread.php?t=1726429

Yeah, the dual-bios feature was the next and last thing I could suggest if that failed which it did due to flash descriptor lock. Anyway, now you can update to v9.0.31.1487 if you want. Just keep away from v9.1 in the future.