2 packs run more efficiently than 3 with the apu, there is enough volume of air to run 3, but they will not run or cool as well as 2. Have a look at the duct pressure when operating 2 then 3 packs you can also (in the flt deck at least) hear the change in air coming in.
Most times you pick up an a/c from maintenance you will find we only have 2 packs on.