The thing about the different ports may be related to the fact that the second stage hose is shipped attached to the bottom port. It is because it fits in the box better and is normally moved to one of the radial ports on assembly.
If you buy a reg from a shop, they should put it on a magnahelic to verify that it is tuned properly from the factory, which sadly is not always the case with all manufacturers. You should be able to easily tell the difference between when the external adjustment screw is in or out.
However, sounds like you have two issues, positioning and depth. Depth alone might indicate another problem.
One of the documented issues with atomic first stages is associated with the environmental sealing with cristolube. If the regulator was environmentally sealed with cristolube and that was removed, but the solid rubber ring is still in place, it will not function properly at greater depths. If the cristolube is still in there, you should have a solid rubber ring. If it was removed or was never there to begin with, it should have the rubber ring with the holes.
So, if there is no cristolube, but a solid ring, you may have a problem. This happens when the customer does not want to pay the extra amount to have a serviced regulator resealed with cristolube, but the technician does not exchange the solid ring for a ring with holes.
This prevents the piston from getting assisted by the ambient water pressure. My understanding is that this is most notable in colder water.
This would not be affected by a horizontal versus vertical position, so not saying that is your issue, but are you sure it was brand new and not a return or demo?