Just wanted to chime in with another data point, as I'm experiencing this issue with a new build as well. Here's the specs of what I've just built:
OS: Windows 7 64-bit
MB: MSI Z97-GAMING-5
CPU: Core i7-4790K with no overclocking running a MASSCOOL 8W2002B1M4 CPU fan (probably only marginally, if at all, better than a stock cooler)
RAM: 8GB (2 x 4GB) G-Skill Ripjaws X Series DDR3 1600
GPU: MSI GTX 970 GAMING 4G
First off, I don't intend to overclock this CPU (at least right now) . I opted for a CPU cooler that wasn't stock only for ease of installation. But I did want the flexibility to possibly explore this down the road at a later time. Unfortunately, any kind of stress testing using a variety of programs (Prime95 v26 and v28, OCCT, etc) results in core temps upwards of 95-100C in most cores without any overclock (aside from the the turbo boosting that happens stock). I've reapplied thermal paste multiple times just in case to verify the install with absolutely no change whatsoever. I was also able to get a replacement CPU from Amazon.com, but it exhibited the same behavior (if not slightly warmer actually). I'll probably end up sending the new one back since it seems to be marginally even worse. I can post some OCCT results later tonight if it would be useful.
In an effort to remedy the issue, I ordered a Scythe Mugen 4 as suggested further up the thread, but it unfortunately won't fit in my build because the fan interferes with the RAM heatsinks on my Ripjaws. It's going back, and I've got a Cooler Master Hyper 212 EVO on order now that looks like it should clear the RAM better. We'll see what kind of difference that makes when I receive it tomorrow.
But this whole scenario is really pathetic. The whole point of buying a K "unlocked" CPU is to have the flexibility to overclock with some better-than-standard cooling. But it seems these CPUs (or at least a certain batch of them), needs much better-than-standard cooling just to operate under their normal thermal requirements! I'm tempted to return the CPU, but I'm not sure what I'd get in its place. Do the locked i7-4790 CPUs suffer from the same troubles? I've never really been into overclocking (and honestly know very little about it), so if swapping for a locked CPU makes this problem go away, I might just consider it.