I have noticed that shipping container's capacity is lower if facing north or south. If facing east/west it is the full capacity that item vaults have, yet if they are facing north or south then they have either 1, 2, or 3 times the volume plus 1 for each additional.
For example, I have my create mod with the item vaults having 32 stack capacity. Facing east/west a 3x3 has a capacity of 288 stacks like it should. If facing north/south then it has a capacity of 102. This is a 1x3 plus just one stack for the additional 6. So 96+6. A full 3x3x9 container has a capacity of 918. Which is 3 9x9 plus just one stack for each of the other 54. So 864+27.
So it looks like it is looking for the 1x3 2x2 and 3x3 combos in only one direction and that is east/west.