Car 'shaking' when in gear. Options

[rentaspace]

Okay, so recently I got my celica back from the dealer after they replaced the front and rear engine mounts, passenger side transmission seal and a bolt that was missing from underneath...

Before going in for repairs the car would clunk when put into reverse, and the nrma mechanic said this was caused by the engine mounts being cracked... Well it still rocks a bit into reverse... But the main problem is, when ever it is in drive or reverse (it's an auto), the car will shake causing everything loose to rattle, it is also very noticeable through the steering wheel
As soon as I start driving, the shake is gone and everything is smooth... But when I go to break at a red light, when I hit about 10km/h the shake starts again, and get worse once stopped...

I have no idea what could be causing this and am just wondering if anyone has any suggestions before I take it back to the mechanic tomorrow
I think it's transmission related but I may be wrong...

[travisxcore]

x3 for motor mounts. After I did my trans swap and put all new motor mounts on my car vibrated like crazy. I didn't have half the dash in either so it amplified it. Was crazy loud. haha. After a while it quiets down a lot. You just gotta break them in is all.