Hi there,
what are you attempting to BOOT from the USB Drive?
Are you trying to install an OS from the USB Drive if yes which OS is it?
Do you have any hard drives installed on the motherboard and if yes, is the controller set to IDE/AHCI or RAID? Also what are the make and model of the HDD's?
I have successfully installed Windows 7 and Linux from a USB stick onto a couple of these boards using the F3 BIOS and the only time I have encountered the "Boot error" message appearing after the "Loading Operating System" message has been due to the HDD I was trying to install onto, not being recognised by the Windows 7 OS. I had to initialise the disk on another PC before I could go any further.
At first, I wanted to boot
http://partedmagic.com/ in order to perform 'off-line' file system checks... To make a long story short, Ubuntu 10.04 and subsequently Linux Mint 9 (which I installed via a Live DVD) seem to have trouble completing mandatory file system checks in certain cases. So I needed some way to boot from a Live distro of some sort to check the file systems. I decided on Parted Magic because I was familiar with it from a completely different situation and thought using a Flash drive would be more convenient than a CD/DVD. In order to do this I downloaded UNetbootin. I've also tried creating a bootable Flash drive following instructions provided by
http://www.sysresccd.org/ and
http://www.ultimatebootcd.com/. As well as using UNetbootin to boot FreeDOS. All of these worked fine on my laptop (an MSI GT735), but fail on the GA-785GMT-USB3.
I'm presently booting from an 80GB Western Digital WD800JD-32HK. I also have two 500GB Seagate ST3500418AS in a RAID 1 Array. In my case I decided to set the controller to RAID. If it's important, I tried toggling the "OnChip SATA Port4/5 Type" from "IDE" to "As SATA Type" (and back again) just to see if that might have any effect. It didn't.
The system boots fine, I'm using right now. :-) I had no trouble installing Linux Mint 9 from DVD... Well except I had to disable the "Onboard USB 3.0 controller" for a time (which I have toggled on and off during my troubleshooting). IIRC, udev and the the xHCI driver weren't getting along after installation. Once I updated one or the other, the kernel panic(s) I was experiencing went away. Anyway, there don't appear to be any incompatibilities between the hard drives and the BIOS.