Ok so retain layer size isn't working as I expect.
I have created my layers in photoshop which are objects with transparent backgrounds. I import to after effects and choose 'retain layer size' but when i place the layers in a comp they are all have the same size bounding box and the centre point is the centre of the comp. How do I make my layers so that they are cropped to the size of each layer e.g. one layer is a wheel and I want the box just around the wheel with the centre point in the centre of the wheel. Also the layers are not importing in the right order.
It works as it should. You simply have your logic backwards. By default AE will import all layers cropped and with extraneous transparent areas removed. Enabling the retain layer size option will do exactly the opposite - keep the transparent pixels. The rest is unclear. When imported as a comp, layer order should not change at all. This might perhaps relate to some groups or smart objects being converted to pre-comps, but without more info and screenshots we really can't know.