First off, I'd concentrate on being able to boot a DOS USB drive as it's loads quicker, doesn't require you to constantly burn CDs and is a very useful skill for installing various other tools should the need arise.
The link from pendrivelinux is what I used and it works perfectly. When you're booting your system, are you selecting the USB drive from the boot menu or are you relying on your system booting the CD drive first?
Is your board actually a 990fx extreme 3? I can't find a 99fx on ASRocks website? Eitherway, I believe pressing F11 on boot should bring up the boot menu and let you select your USB drive.
I try running atiflash unlockrom 1 and I get "Invalid command?!
unless you omitted it from this post, you need a hyphen before each command... so you'd probably need to type:
atiflash -unlockrom 1
Do you have 2x cards in your system? The number there isn't related to the physical PCI-E slot the card occupies in the motherboard, just so you know!
Hopefully I won't get into trouble posting this here as it's probably copy write info but here is the output from the help of atiflash for reference (I couldn't find it online to reference with a quick google search):
--- ATIFLASH v3.99 ---
-h, -?, /h, /? Help (this screen)
Format: ATIFLASH [command] [parameter1] [parameter2] [parameter3] <option/s>
-i [Num] Display information of ATI adapters in the system.
Display information of adapter [Num] if specified.
-ai [Num] Display advanced information of ATI adapters on system.
Display advanced information of adapter [Num]
-biosfileinfo <File> Displays the Bios info in file <file>
-p <Num> <File> Write BIOS image in file <File> to flash ROM in Adapter
-pa <File> Write BIOS image <File> to all appropriate adapters.
-s <Num> <File> [Size] Save BIOS image from adapter <Num> to file <File>.
First [Size] kbytes (except for Theater in bytes) of ROM
content is saved if [Size] is specified.
-cf <File> [Size] [Sum] Calculate 16-bit checksum for file <File>.
Checksum for the first [Size] kbytes of the file is
calculated if [Size] is specified.
-cb <Num> [Size] [Sum] Calculate 16-bit BIOS image checksum for adapter <Num>.
Checksum for the first [Size] kbytes of the ROM content
is calculated if [Size] is specified.
-cr <Num> [Size] [Sum] Calculate 16-bit ROM checksum for adapter <Num> and
compare it to the [Sum] specified. This command is
the same as -cb if [Size] is specified.
-t <Num> Test ROM access of adapter <Num>
-v <Num> <File> Compare ROM content of adapter <Num> to <File>
-mi <Num> [ID] Modify SSID & SVID in BIOS image of adapter <Num> to
<ID>. SSID & SVID in BIOS image of adapter <Num> is
displayed if [ID] is not specified.
-mb <Num> <File> Modify SSID, SVID, BIOS Pin Number, & Boot Message in
BIOS image of adapter <Num> to values in <filename>.
Input file example:
ssid = 715B
svid = 1002
biospn = "113-xxxxxx-xx"
bootmsg = "ATI graphic board"
-pak <File> Package an executable for BIOS update according to
the commands in <File>.
Config file example:
outfile = update.exe
banner = "Update v1.0"
infile = a123.bin
command = -pa -padevid=715B infile
-isr <Num> <Build Number> <Board Number> Set ISR number based on the given
build and board number
if not specified, print out ISR Number
-prod <Num> <12 digit serial number> Set PROD number based
on the given serial number
if not specified, print out SN Number
-checkprodsn <Num> <12 Digit Serial Number> Comparing the Prod SN based on
existing prod sn saved in ROM
-f Force flashing regardless of security checkings (e.g. AsicID &
BIOS file info check OR boot-up card).
-fa Force flashing bypassing already-programmed check.
-fm Force flashing bypassing BIOS memory config check.
-fs Force flashing bypassing BIOS SSID check.
-fp Force flashing bypassing BIOS P/N check.
-nw No user interaction on test failure.
-sst Use SST25VFxxx flashing algorithm regardless of ROMID straps.
-st Use ST M25Pxx flashing algorithm regardless of ROMID straps.
-atmel Use AT25Fxxx flashing algorithm regardless of ROMID straps.
-nopci Do not enumerate PCI adapters, i.e. enumerate only AGP and
-pcionly Enumerate only PCI adapters, i.e. do not enumerate AGP and
-agp Enumerate only AGP adapters, i.e. do not enumerate PCI and
PCIe adapters unless used with -pcie or -pci
-noagp Do not enumerate AGP adapters, i.e. enumerate only PCI and
-pcie Enumerate only PCIe adapters, i.e. do not enumerate AGP and
PCI adapters unless used with -agp or -pci
-noisrsn Force to erase existing ISR number on ROM
-noprodsn Force to erase existing Prod SN number on ROM
-nopcie Do not enumerate PCIe adapters, i.e. enumerate only AGP and
-pci Enumerate only PCI adapters, i.e. do not enumerate AGP and
PCIe adapters unless used with -agp or -pcie
-noremap Skip BARs error detection and remapping in PCI configuration
-reboot Force a reboot of the system after successfully completing the
-siireset Specifies the GPIO Pin to be used as the Reset when updating
SiI1930 microcontroller firmware
-siireset=7 <No Spaces>
-siiuprog Specifies the GPIO Pin to be used as the uprog when updating
SiI1930 microcontroller firmware
-siiuprog=14 <No Spaces>
-scansii Overrides normal adapter detection to enable detecting SSI
roms with/without TPI firmware
-log Logs output to atiflash.log, overrides existing file
-logappend Logs and appends output to atiflash.log
-ddc Enable DDC support
-padevid=<ID> Use with -pa command to update adapters of specific device ID.
-passid=<ID> Use with -pa command to update adapters of specific SSID.
-pasvid=<ID> Use with -pa command to update adapters of specific SVID.
-pavbpn=<VBPN> Use with -pa command to update adapters of specific VBIOS PN.
-excl_memtrain_dtable When flashing on new VBIOS, a pre-determined memory
training data table in the old VBIOS will not be
-isr <adapter num> [build num] [board num] If build number and board number
are specified, sets the ISR Number
value in specified adapter.
If only adapter is specified, the current
ISR Number is displayed
-checkpn <adapter num> <filename> Checks PN of the current product
and compares it to external file
*<Num> = adapter number, <File> = filename
*[Size] = data block size in KBytes, except for Theater Pro in Bytes
*Use command -i to see the adapter numbers in the system.
*Theater Pro supports commands -i, p, s, cf, cr, t, v and options -f, -noremap.