Five bays is fine, as long as they are all on the same ship.
Try splitting that five-bay transport out into a seperate fleet, then loading the Engineer. If that doesn't work, try quitting to desktop and reloading before attempting to load the Engineer.
If you created the five-bay transport by using SM-mode to modify an existing ship, you will need to open the "Ships" window and click on that ship to refresh the data, before any changes actually take effect.