Once in a while, the game pauses, it I had to left click for it to return to normal

Whenever I play minecraft, the game always pauses about every 3 minutes. I'm able to see the mouse, and I'm frozen. This is only fixed when I left click, however, it will keep happening. I looked into this on google and found that I need to go into .minecraft/options.txt. It said to put pauseonLostFocus from false to true, but this makes it go to the game menu instead of the game pausing. I don't know how to fix this problem. Thanks!