|"once you weed through the misinformation on the Internet and nail down the correct utility setup to run the flash procedure"|
What's to weed thru? If you have an ECS board so you should get the utility, BIOS file & instructions from the ECS site. If you have an ASUS board, get them from the ASUS site. Gigabyte board? Use the Gigabyte site...etc, etc, etc
I didn't think the BIOS update would do anything. I think you should stop relying on a software program (BIOS_AGENT) to tell you what's out of date or not. It's 2009, do you think the software knows that the final BIOS update for your board was in 2003? All it does is compare dates...it realizes that the BIOS is 6 yrs old & that's all it knows.
This statement written by Skip is very important: "I'm amazed that thing will boot with pci/agp busses that far out of spec." I agree 100%. Default for PCI/AGP is 33/66MHz, 37.5/75MHz is generally considered the safe max. Some devices will still function with the buses slightly higher than than that, but 44/88MHz is just too far out of whack. The sound would be crackling, video would be messed up & data would quickly corrupt on the HDD. Your board officially supports 533MHz FSB so that means when the jumpers are properly configured, the PCI/AGP will run at 33/66MHz. I think you're just the victim of crappy software.
Are you sure you have all the jumpers properly configured for the type of RAM you're using?