I suppose, you have got the Y dimension set to 1 and the Z dimension (in the object dialog) to something > 1, is that correct?
You probably just need to switch those two values.
The X and the Y dimensions each designate indices for an individual logical place while the Z dimension just specifies how many parts you will be able to stack on one such place. And your picture pretty much looks like stacks that are just distributed in X direction.
The plane selection in the 3D dialog talks about spacial dimensions in contrast to the logical ones I just described.