When i first installed the stock heatsink that came with my CPU, i had Bios ver F9 (latest non beta bios for my GA-Z87X-UD5H) that was the first bios supporting the 4790K (and in general Haswell-E cpu's) for my mobo. When running Prime 95 or other test my temp from idle 35C, skyrocketed in just a second to 100C (and thermal throttling started kicking in).
Then i gave a try to F10c bios (which was stated as STABLE-BETA) and accompanied with a strange "Enhanced Intel K-sku CPU performance" tagline. When i installed the bios, i noticed that the CPU wasn't anymore skyrocketing to 100C in a second. It sure reached this temp with Prime95 (and only with prime95) but it did this more slowly and progressively like sometimes 1 minute or so.
So...
GA-Z87X-UD5H F9 (ALL STRESS TESTS) 35C ----> 1SEC ----> 100C ---> THERMAL THROTTLING
GA-Z87X-UD5H F10c (ALL STRESS TESTS - EXCEPT PRIME95) 35C ----> 1HOUR ----> 85C ---> NO THERMAL THROTTLING
GA-Z87X-UD5H F10c (PRIME95) 35C ----> 1-2 MIN ----> 100C ---> THERMAL THROTTLING
So surely there is a big connection in how the bios handles the new processor, but this is not the only culprit for high temps. I believe that with new bios versions from every mobo manufacturer we will see big improvements in temps. I am sure that in their secret underground labs, as we speak, they are doing tests trying to correct the problem as much as they can from their standpoint.
Also i must highlight again, that the above tests were done with stock intel cooler and 2-3 days after installing my new CPU. Being disapointed by the thermal performance of stock cooler i bought Η100i.