You're fine :-) Apparently M5A99X-EVO-R20-ASUS-1302.CAP is not exactly 8MB, which is the size of your flash chip (W25Q64). This is just a simple sanity check flashrom uses to help prevent flashing the wrong file to your chip.

I took a quick look at a BIOS image from Asus' website and it appears that they append 2KB to their BIOS image:
007ff060  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
00800780  50 45 49 45 2b ac f5 ff  10 00 00 00 00 00 00 00  |PEIE+...........|
00800790  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
008007f0  e9 0d e0 ff ff 00 00 10  00 00 78 56 00 00 f0 ff  |..........xV....|
00800800

Usually this junk vendors append to their BIOSes is benign, but you never really know... I recommend looking around to see if anyone else has had success flashing this board using Flashrom. I do not recommend bypassing the size check or truncating the extra 2KB unless you have a means of recovering (Backup BIOS ROM, external programmer, etc).

On Tue, Jan 8, 2013 at 5:26 PM, Leslie Rhorer <lrhorer@mygrande.net> wrote:

I don't think I am in any jeopardy, but I need to make sure, because an
attempted flashrom write failed.  In addition, I would like to get it to
work, because it as been recommended I upgrade the BIOS due to issues in
lm-sensors.  When I attempted to upgrade the BIOS, I got this error:

RAID-Server:/RAID/Server-Main/Downloads/Asus Motherboards/M5A99X EVO R2.0#
flashrom -w M5A99X-EVO-R20-ASUS-1302.CAP
flashrom v0.9.4-r1395 on Linux 2.6.32-5-amd64 (x86_64), built with libpci
3.1.7, GCC 4.4.5, little endian
flashrom is free software, get the source code at http://www.flashrom.org

Calibrating delay loop... OK.
Found chipset "AMD SB700/SB710/SB750/SB850". Enabling flash write... OK.
This chipset supports the following protocols: LPC, FWH, SPI.
Found Winbond flash chip "W25Q64" (8192 kB, SPI) at physical address
0xff800000.
Error: Image size doesn't match

        I then verified the flash image against the backup image and it
apparently passed:

RAID-Server:/RAID/Server-Main/Downloads/Asus Motherboards/M5A99X EVO R2.0#
flashrom -v Safety_BIOS.cap
flashrom v0.9.4-r1395 on Linux 2.6.32-5-amd64 (x86_64), built with libpci
3.1.7, GCC 4.4.5, little endian
flashrom is free software, get the source code at http://www.flashrom.org

Calibrating delay loop... OK.
Found chipset "AMD SB700/SB710/SB750/SB850". Enabling flash write... OK.
This chipset supports the following protocols: LPC, FWH, SPI.
Found Winbond flash chip "W25Q64" (8192 kB, SPI) at physical address
0xff800000.
Flash image seems to be a legacy BIOS. Disabling coreboot-related checks.
Reading old flash chip contents... done.
Verifying flash... VERIFIED.

        Am I in jeopardy, here?  How can I get flashrom to properly write
the new BIOS?

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--
David Hendricks (dhendrix)
Systems Software Engineer, Google Inc.