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I read that there is fanduty and autofanctrl command that I can use to control my fan speed. How can I do that on Windows?

We were testing out the EC driver, and we think there may be a data consistency issue around access to the ec from your driver and other bios functions. We see if we do a lot of flash access from the OS, that sometimes the data is not what we expect to be in the flash. @JohnAZoidberg

I think that this may be due to ACPI access to the EC may be interleaved with this driver access. Looking at your driver it seems to be doing direct port io. 

If you look at our EC interface in ACPI it will acquire a lock around any EC transactions. 
Some of these ACPI methods will be invoked to get temperature readings every second or so, for various drivers, for example the intel DTT driver will be reading temperature sensors. And we think these may corrupt access from this tool.

See for example EC0 Method M005
framework_dsdt.txt