You updated your AM2+ motherboard to allow it to work with an AM3 chip. But it is still an AM2+ motherboard so the bios update should not be an issue.
Something else might have changed in the BIOS, they might have tightened memory timings or lowered default voltages. I would try manually setting the memory to a slower speed and see if that fixes the issue. Does it default to too low of a memory voltage?
Maybe you have to manually set the voltage higher. My motherboard will allow DDR2-1066 but you have to manually set the voltage to 2.1V or it defaults to 1.8 volts and crashes a lot. (What memory do you have? DDR2-800?)
Another thing to do is review the voltage settings in the bios. I'm not sure what the X2 6000+ uses for default, but it should probably be around 1.3V.
EDIT: I just found the following:
The stock voltage for the 89w 6000+ is 1.3v to 1.35v.
The stock voltage for the 125w 6000+ is 1.35v to 1.4v.
So if it set the voltage to 1.3 but it is the 125W chip then you might have an issue.