The difference lies in what is preventing the equilibrium. Take gases crossing the alveolar membrane into the blood as an example. Some gases cross the membrane very readily, but do not dissolve well into the blood. In this case, higher rates of blood flow would cause more gas to be picked up and dissolved. The restriction is the amount of perfusion, so this is an example of perfusion limited.
On the other hand, other gases do not pass the alveolar membrane well, but are readily absorbed into the blood. In this instance, gas movement is restricted by the rate of diffusion across the membrane, and therefore, this is an example of diffusion limited.
