I think, in your particular case ... with leaking intake gaskets ... that it has to do with engine load.
If the engine is not under any load, (not in gear) it would maintain enough port velocity to deliver a lean fuel mixture ... but still enough to make each cylinder "carry it's weight", at least partially. The momentum developed by the "good" cylinders would also help to carry the ones not making a full contribution.
Once you drop it in gear ... the load increases, the port velocity decreases, and the momentum effect is largely absorbed by the torque convertor. Those cylinders that are not carrying their own weight are much more of a liability now ... and idle quality suffers.
Similarly, if you have a header gasket leak ... you don't notice it nearly as much until after you drop it into gear and put a little load on.