I have a Brother Innovis 5000 but the needle down light flashing then shutting down the machine brought back many 'not so fond' memories for me. I had something similar happening with my machine and had no luck describing it to the repair technician over a period of about 18 months so it continued to get worse, and then much worse over time. Finally, I watching the light flash red to green, red to green, every time I wanted to sew. By then the repair technicians were as frustrated seeing me as I was with the overall situation.
Finally they broke down and called Brother directly with me present to hear the conversation; bottom line - the switch where the foot pedal plugged into the machine was faulty. Once it was replaced - machine works great! There is a test the technicians can run to test the pedal as well which probably should be done. The key for the technicians seemed to be the flashing needle down button.