Here is what i would do, it may or may not be the best way, not sure on that, only what i would do.
First i wouldnt do a bios update unless i read at the website that a certain bios update involved hardware updates.
Next i would take out all items from my pc setup that i absolutely dont need, pci cards, usb items. Get the system down to one stick of ram (unless you are running rdram), video, keyboard, mouse, monitor, floppy drive, main c hard drive and thats all for now. That means any cd or dvdrom is to be disconnected and that also means you have to check your main c hard drive jumper settings as often when its set as master with a slave (slave being cd or dvd rom or burner) then the jumper setup is one way and when the hard drive is running alone without cd or dvd rom then its a different jumper setup, for example western digital is no jumper at all when all alone on ide connection.
See if your system runs ok at this point and do let us know what you were able to take out from your system.
If you still have problems then i would update all drivers one item at a time. Turn pc off, not just reboot for each new set of drivers and check system to see if problem is still there.
While doing all that, check all connections, vid card, ide or sata drive, etc, etc.
This is a heck of a lot of work but as far as i know its the best way to find out what the problem is.
If you should need the bios upgrade we can help you with it. You downloaded the rom, which is the upgrade itself, but you also need to download the actual program (utility) that does the job for you, so go back to website and download that, although, as i said i dont see why at this point. Its not a good idea to try fixing an issue with a bios upgrade when there is no proof the upgrade will fix the problem. Bios upgrades do fail, and they render a mobo useless and with issues already its a bet that the odds increase of a bad bios install, so i dont recommend it. But when the system is working well and if you still want to do it, or if you find a good reason to do so, then by all means we will help you. We will help you even if you want to do it now, lol. No dis-respect intended.