Old Mac Pro shut down pop up on boot.

I have an old Mac Pro (Early 2009 Intel 2x 2.6 Quad Core Intel Xeon) running El Capitan. Today when I booted up it immediately came up with a pop asking if I wanted to shut down. When I cancel it pops straight back up again. I have tried booting up in safe mode, flushing the pre ram and even changing the keyboard but to no avail. What can I do to fix this?