Set it for pwm/auto.. .
Yes, it's possible for SpeedFan to mess with it, if you changed SpeedFan parameters, which you did only after the issue started. But even if SpeedFan was set to the wrong address for the cpu sensor, and reads a negative number, the fan would still run at minimum rpm. If you disable SpeedFan, so that it doesn't automatically startup with windows load, then it can't affect the fan profile until it does, bios/windows will set profiles until software changes them.
There is no switch in any bios to turn off a cpu fan. There's eco modes, silent, performance etc but none will set a duty cycle to 0%. DC will usually only go as low as 40% (5v) and pwm might see 20% (still 12v), but even graphic fan curves will have a flat line minimum rpm. Sys_fan headers can have the ability to go to fanless mode, but that'd require the cpu fan itself to be hooked upto a sys_fan header, not the cpu_fan header. That would explain lack of changes by software, as the software would be trying to change the cpu_fan header parameters, not the sys_fan headers. I'd visually check that the cpu fan is actually on the cpu_fan header and correctly mounted.