I have a VF-3 SS APC and have had no problems like you are having. What might be happening is when you machine pallet 1 it thinks its machining pallet 2. When you are in current commands while running the program does it say "Pallet 1" below the code area of the screen. The way I program the APC is setting up a master program that is simply the pallet changes and subprogram calls. If "Pallet 1" isnt showing up below the code then I would start the program with a Pallet change to pallet 1 so the machine knows that pallet 1 is currently in the machine.