I am not sure why I started having this issue. Probably my TV is getting older. When Raspberry Pi tries to put the screen into screen saving mode or something, it flickers like crazy.
I thought that it was the screen-saver but later I figured it is "blank" features. I am still not clear what it is and why it happens but this change fixed my issue at my case; BTW my TV is samsung 1080p; I think it was 47inch or something.