Screen blinks or flashs occasionally

Here is a very weird issue:

Screen blinks or flashes occasionally. The flash stops completely when I plug in thunderbolt-vga adaptor. (Even without connecting an external monitor). It returns when I remove the adaptor.

When I boot from one of the Linux live distros, it does not blink. It works perfect. However it blinks when I boot from OS X recovery usb media. I have another Macbook air 2013 which I used to test if the screen is the issue. I connected the 31pin display connector of the '11 to the '13 display, and it worked perfect, except the blinks. I have tried resetting the SCM and NVRAM to no avail. Please help.