You could be running out of ram, in my experience with games like minecraft etc where you can set the amount of ram utilisation, when it hit the maximum allocation the whole system will freeze or drop frames for a moment to recover as much memory as it can and then continue until it happens again, usually becoming more frequent over time.
What are the temps youre getting when you see this happen?
What game are you playing?
See if you can download msi afterburner or some sort of tool to monitor cpu usage, temp, power, ram usage, gpu usage, power, gpu memory over time and see whats happening when the drops occur