IMO, this can still point to a improperly mounted CPU cooler/TIM (gawd do I ever hate stock Intel coolers "pushpins" mounts, I can never tell if it's mounted right.) The previous two CPU/MB mounts I just ditched the stock cooler with an aftermarket one, and when I removed the MB I kept the CPU and heatsink mounted because I didn't want to take all that gear apart again. Right now I'm using a haswell with a stock cooler (not stock TIM however, and it hasn't been delidded.) I haven't had ... well any of the problems people are frequently mentioning beyond the occasional crash after several hours.
If the TIM is uneven or the cooler itself isn't flush against the CPU, then it's not working efficiently, or your pumping system isn't working. You can try
http://www.alcpu.com/CoreTemp/ and see if the CPU's are all heating at the same rate. (click "more downloads" so you don't have to download the other junk just to install it. It doesn't need to be installed, only run.)