Trany alignment?

I changed the front engine mount ( front of the car, side of the engine) because the car was shaking ( that I lied though) and the engine light kept coming on. Also at stop signs I would get a thud from the tranny.
After changing the mount everything was ok for a awhile then after stopping at a sign and then mashing the throttle I heard a smaller thud and the engine light came on again.
I lifted the car by placing the jack under the engine mount, the one that I changed and to see if a bolt came loose.
I put the car down and everything was OK again
Then the same thing happened after stopping at another stop sign.
I raised the car from the same point again , lowered it and all was ok again, until you guessed it...the stop sign.
Is the tranny out of alignment with the engine?
Am I realigning it right when I lift the car?
How do I fix this problem?