Check temperatures. You can do that using HWMonitor. http://www.cpuid.com/softwares/hwmonitor.html
Make to check them during the lag, not while idling on desktop.
Thank you for the suggestion.
All the CPU cores are at a lower than normal temperature.
During the lag, max CPU temperature for all 4 cores is 53 degrees Celsius. Before, the CPU normally reaches 80 degrees Celsius when playing Minecraft and other games.
Hard drive maintains a steady 33 degrees Celsius.
GPU was not shown on CPUID HW monitor so I had to use GPU-Z;
GPU reaches 60 degrees Celsius maximum.