mine did this as well right after i replaced my tranny. I've noticed that the E34's suspension doesn't like to be unloaded for a prolonged amount of time, seems to make things loose. For instance i got new tires today, and while it was up on the lift for only about 30 minutes, it did clunk quite a bit right after, and after about 20 miles it returned to normal for some reason. Drive it a bit more and see what improves.
1995 540iA M-Sport - 76k miles. 1 of 1 auto AW3 cars.
1995 540i/6 - Misc Parts donor for above.