I have a similar problem that drives me nuts.
I increase the Turbo Core settings for my FX-8320 to some higher levels. I save the settings as default, but after a restart they're reset to normal.
If I check "apply my last settings when system boots", Turbo Core is always completely disabled on the next boot.
If I start AOD manually and load DefaultConfig.xml, everything is fine.
Increasing the CPU multiplier seems to stick, but that needs to disable Turbo Core for it to work properly, and I need that for my single-threaded stuff.
It's just silly.