After putting the copter together over a few exciting evenings, initial test flights showed some very strange control responses with pitch and roll being swapped. I could "correct" this by swapping my Aileron and Elevator receiver channels, but that made the autopilot's stabilization input completely unpredictable. I checked my wiring and documentation, and found the following:
The PDB that comes with the 3DR-B is oriented to use rotor 2 and 3 as the quad's front in x-mode. See page 7 of this doc:
The APM2, however, thinks that rotors 1 and 3 are in the front:
So, wiring the PDB correctly and hooking it up to the APM2 results in a copter that has its motors turned 90 degrees from its board. The solution is simple enough.
Maybe this is a well-known issue... It was news to me. Or maybe I've missed something obvious in the the build process. If your newly-built quad is behaving oddly, look into it.
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The fact that the X-mode forward arrow is nearer to motor plugs 2 and 3 doesn't mean that those are the front two motors, it's just showing the direction the board should face. When you go to plug in your motors, you should still plug them into the motor positions referenced in the page 10 diagram, 1 and 3.
I did notice this on my quad build but realized that the PDB has no influence on the orientation except as a mechical reference to the builder. It is important, of course, to make sure the correct ESC wire is going to the correct motor via the PDB. That could be confusing as you point out.
As a reality check for those not flying yet (meaning me too), use a meter to confirm the continuity from the APM ESC output to the appropriate ESC.
I think you may be reading the PDB lettering a bit too literally. All those sources show the same motor order, it's just the PDB is offset by a few degrees with placed in the quad in X mode.