No, I triplechecked that I was booting from the backup HD and the BIOS is not injected. I selected the USB hard drive from the boot menu of my Mobo BIOS and I have the backup bootloader set at 1024x768 and the main bootloader at 1920x120. So, the difference between both is HUGE, therefore I can tell which disk I'm booting from.
maybe your backup installation was booted by the chameleon on the main hdd where the vbios was injected?
The only settings in common between my two bootloaders is the PciRoot=1 and GraphicsEnabler=1. I don't know if PciRoot=1 has some effect on this.
I have attached a screenshot of my system profiler showing that my BIOS version on my backup installation is "XXXXX - internal" and the contents of the com.apple.Boot.plist for the backup HD. Notice that with either injecting the bios or not, on the Screens preference pane, I have HDTV resolutions available to select.