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Just to confirm, this issue only happens when you run Windows 8.1 but it doesn’t happen when run Linux, correct?
Are you running dual boot? Where are you seeing this behavior?
Can you access Windows at all? If so, is it possible to run the Intel® Processor Diagnostic Tool
Intel processor has power saving that decreases the CPU frequency when the CPU is not in use, if this is not the case check if there is a new BIOS version for your motherboard and update the motherboard BIOS.
You can also, try accessing the BIOS and disable the speed step, I’m not sure if this is the same name in the motherboard BIOS you have but you may want to check your motherboard BIOS manual or contact MSI support for you to get the proper settings at the BIOS. You should be able to get the manual and support here:
NOTE: This link is being offered for your convenience and should not be viewed as an endorsement by Intel of the content, products, or services offered there.
Please let me know how it goes.