Howdy Kaz,
No expert here but my 1st guess would be when you updated your BIOS that your AGP aperture setting in the BIOS was somehow changed below the size needed by your vidcard and therefore Windows decided to use PCI mode by default. Reboot your machine and use whatever keypress you need to go to the BIOS and look for AGP aperture size, probably in Chipset Features section and set it at least to the amount of memory on your vidcard, preferably larger ie. twice that much and then test it for stability. I have had this happen with another setting in the BIOS on an older machine that completely hosed it and nobody from Tech Support at MS could help me because they aren't allowed to tell you to go into the BIOS or recommend that you do anything in there expressly because you can hose your box if you screw around in there. Catch-22. This was before I knew very much about computers and was so frustrating and infuriating that I vowed to learn enough to build my next machine myself. Havent spent 1 minute on the phone with a Tech Support "professional" since, thankfully. My ears start to smoke just thinking about it.
Anyways, try that and see if it helps and perhaps someone who knows more than I will post in the meantime. Good luck!
kbman
Oh and BTW, whenever you have any type of question about your machine you need to post ALL of your specs for ALL the hardware in your box and anything else that could possibly be related to the issue at hand. This allows people to actually give you an answer that could be a solution. Otherwise it's all shots in the dark.