when i brake i find car shaking but when ii begin driving it back to normal what could this be?

i have a pontiac aztek and it recently had a new computer put in due to how i was braking at a red light and the car would suddenly make an acceleration noise then the reving would go back down. and so on. now everytme i stop at a light, while pressing brakes, the car begins to shake but when you let go of the brakes it runs and shaking stops. what could the problem be