Hi! I got a hyper 212 cooling a 2500k OCed at 4,3 ghz (1.27 Volts) that drops down to 1,6 ghz on idle to save power. I noticed that there was quite a big temperature difference between the cores. Here are my temps:
Sometimes, the ΔT between cores can be as much as 10°C. I remounted my cooler 2 times, tightening the screws in a cross pattern. The backplate is perfectly flat and so is the cooler base, so no problem here. As far as TIM, I used the coolermaster one that came with the cooler and I use the small dot method to apply it on the CPU. When I removed the cooler, the TIM was spreed out correctly (in a big circle covering the whole CPU).
Should I be worried or is it normal?
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It's normal. Don't worry about it. Mine is nearly identical, in fact (1st core the coolest and 2nd core the warmest, but by a 2C or so smaller margin).
Since they run independently and are designed to handle different loads, they will generally differ in temperature. There's no reason to be alarmed.