According to Hardware monitor professional my cores are running at >90 Celsius. Is that normal?
I am using the cooler came with the processor. This happened when I used Xilisoft video converter. Should I stop using my computer or this is happening due to a bios bug. My mother board is Intel DG41RQ
You'll need to turn off the computer. Remove the HSF and clean all of the thermal compound off the cpu and HSF (use rubbing alcohol to help remove the thermal compound).
Then get some arctic silver 5 thermal compound, put the right amount on the cpu, then place the hsf on cpu and make sure the all the push pins were fully down.
Your problem is probably when the HSF was installed, the one of the push pins was not pushed all the way though. When this happens, the hsf does not have full contacted to the cpu and so cant do it job.