I would check for a bios update. It definitely seems related to a bios issue. Could even be something as simple as a bad CMOS battery, but generally that would just reset you to default settings instead of vastly underclocked ones.
How long have you had this setup before these problems started? Did you do anything prior that could have triggered this behavior? For example if you removed the CPU and it bent a pin it could cause similar issues. If you have not altered anything about your system and the problem occurred, then I would check for a bios update.
If there is no bios update and the problem persists I would try reaching out to your motherboard manufacturer. I just don't see this being a CPU related issue.
I would also recommend updating your chipset driver which you can find here; http://download.msi.com/dvr_exe/intel_chipse_9_w10.zip
TGrable, thank you these suggestions.
I updated the chipset, which kinda worked out, now my CPU is always on 4000mhz only dropping to like 3700mhz for some seconds when idle. Temp is still low around 37c.
Bios is up to date.
I have contacted my dealership over phone and they are unsure of the problem and want me to send in both my motherboard and cpu for testing.