Yeah I'm actually having the same exact problem with my K8N Diamond Plus/Opteron 144, and have been searching the web to to avail. I also upgraded with MSI Live Update 3.
Bios settings do nothing to change clock speed, checked with multiple programs.
ClockGen detects PLL, PLL sliders work, but ClockGen and CPU-Z both show default clock speeds and multipiers.
Bios still shows my settings changed, but clock speed remains default. However DDR speed seems to be affected by FSB settings but only within the bios. POST screen and CPU-Z both show default 400mhz speeds.
Getting to be a real annoying problem