is my trans taking a dump?

Well valves have already been adjusted. After break in. I have checked for intake leaks and found nothing. Like I said it only does it in gear and idle. And makes a vibration through out the car and disappears once it sees a little rpm. Runs beautiful otherwise. Doesn't make sense that it would be the motor when the trans engages then causes a kinda like thumping noise, and shake. I think reverse seems to be a little worse than forward gears