I need help

When I first start the car there is a thumping sound that I can feel through the brake and the transmission. When I step on the brake the thumping stops, when I let my foot off the brake it thumps again. It does not thump while I am driving either.I noticed the middle brake light also flashes with the thumping noise and the "Check Engine" light is on. It only does this while the car is idle. Is this a brake switch problem? we've already changed all the brakes etc.. but can't figure this one out.
Thanks in advance for any help
Edited by: wabbit on Mar 8, 2010 1:02 PM