First, there might not be any reason to upgrade your BIOS. In fact newer doesn't mean 'better' and the only reasons to update your BIOS are as follows:
1. CPU requires newer BIOS version
2. Non-OS Instability
3. Peripherals e.g. 2TB HDD requires new BIOS.
4. Memory compatibility ; where current RAM is causing errors or stability.
Also, ASUS has made the transition from (.ROM) to (.CAP) requiring their 'BIOS Converter utility' which is for Windows 8; more information see this PDF -
http://dlcdnet.asus.com/pub/ASUS/mb/LGA2011/P9X79-DELUXE/BIOS_Converter_User_Guide_for_X79_series.pdf
As far as updating the (.ROM) with either ASUS USB Flashback or EZ Flash 2 I always begin with a bootable FAT 32 Flash Drive:
Open and run CMD as Administrator.
Type Diskpart, press Enter.
Type List Disk, press Enter.
Type Select Disk # (where # is the number your USB drive in the list), press Enter.
Type Clean, press Enter.
Type Create Partition Primary, press Enter.
Type Active, press Enter.
Type Format Quick FS=FAT32, press Enter.
Type Assign, press Enter.
Type Exit, press Enter.
Preparation, download the (.ROM) file, extract from (.ZIP) and rename to --
SABERX79.ROM then copy to the Flash Drive. Make sure the PC is off, PSU is plugged-in (standby power) and at minimum the 24-pin main is connected to the MOBO from the PSU, connect the Flash Drive to the
White USB port and press the USB BIOS Flashback button. The button will start to blink within ~5 seconds and the process takes 2~3 minutes.
More information see - http://event.asus.com/2012/mb/USB_BIOS_Flashback_GUIDE/
Currently, I see no reason to convert from (.ROM) to (.CAP) with anything but Windows 8.