Some things to check, When you update the bios, certain settings get factory reset. When the system shows the Jmicron screen, does it show a drive at all? or does it show nothing.
Is your boot order set to start with the jmicron drive?
This is just for illustration, but it should look like this but showing jmicron, Gigabyte changed it, but it is a jmicron controller too
http://img19.imageshack.us/img19/9740/jmicron.jpg
If you see no such thing, maybe your jmicron controller has been shut off or set wrong.
Enter the bios, Under Advanced select Onboard Devices and then see if you Jmicron SATA/PATA controller is set to Enabled. setting it to IDE mode may be an idea, but its not needed if your drive on it is an IDE anyway.
Save your settings and restart then reenter the bios and go under Boot then Boot Device Priority and see if your drive is in there, if it is, set it to the first boot device.
Since I do not have your board here to play with, i am going by the manual. I hope this may help you see if there is a issue there.
If that does not help, you may want to flash back to the first bios that listed support for your new CPU. I have seen bios flashes break things like that. In fact once Asus broke a VIA controller(K8V SE) in such a way that it would cause system wide pauses for about a second or so every 20-30 min. A quick flash back and it was fixed.