if the above instructions don't resolve the issue:
i run handbrake as well as a number of other video editing programs, and have an intel i7-4790 (not the K) cpu, and had the same problem, running temps of 99-100C - and i only discovered it by accident, as my Asus monitoring utility was showing 67C max. When i ran other temp monitoring utilities they showed the 99-100C but i assumed they had to be off, as Asus had to have a better handle on temp monitoring on their own board - WRONG
There have been overheating issues with the 4690k, 4790(k) and a few other cpus - and there are a couple of good threads on intel's community website. There's a link to intel's XTU (Extreme Tuning Utility) that does a good job of monitoring temps, as well as the ones mentioned above
1st one:
Troubleshooting Intel® Core™ i7-4790K / i5-4690K overheating https://communities.intel.com/docs/DOC-23517
2nd link:
How best proceed with overheating i7-4790K?
The 2nd link is a 38+ page thread - ignore the first 15 or so pages, early releases of the 4790K apparently had qc issues, but appear to have cleared up by October 2014
biggest item that helped me, and i only tried the suggestions in desperation after re-applying heat sink thermal paste 2 times, was intel's suggestion to clear the CMOS and un-install the motherboard utilities - when i uninstalled Asus's performance monitoring utilities, temps improved some, but not that much - when i cleared CMOS, temps improved dramatically.
Handbrake is still the program that generates the highest temps, but max i see now is 80-82C and even then, those are only short duration spike temps
and if gives you any peace of mind, i ran my cpu at those temps (unknowingly) for 2-3 months, with some of the video files taking 3-4 hours to render. The cpu has throttling limits built in as "safeties", and one of them is "thermal" or heat limiting - when temps would hit 100C, the cpu would auto throttle the current to drop the temps, so that pretty much saved my cpu from frying.
Intel, in their charts indicates suggested max operating temp for the 4790k cpu to be 74C, +/- 4-5C, so that's what i shot for. I had other issues, mainly a small form factor case, that i've resolved by installing additional fans pushing more air in, and installing a better heatsink/cooler (noctua)
hope that helps