While troubleshooting another issue with APM, I noticed there was a pair of pads unused on the board. One pad is connected to pin 1 (PG5) of the ATmega1280 chip. The APM schematic shows there is a 1K resistor (R8) connected to pin 1 (the other pad connects to the MUX 1 pin of IC3).
My R8 is missing. The pads are located near the corner of the ATmega chip where pins 1 and 100 meet. There is another resistor right beside it.
Can someone tell me if your APM board includes R8?
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It's supposed to be like that. Mine is the same way. It is was a 1k resister from the PG5 to the Mux select pin on the output multiplexer. The mux select is also connected to an output on the 328 fail-safe/PPM converter chip. I think this was a hold over from the original Ardupilot. It had the ability to "override" it's fail-safe chip from thru software when the fail-safe chip was in manual mode. The software could "force you out of manual if it wanted to. The output of the main 328 processor could force the mux select low when the failsafe chip was high. The fail-safe chip would get warm due to it's internal pull-up resistor being connected from V+ to ground, but it worked. With the APmega when you are in "hardware manual" It cannot be over-ridden. I don' think most people even use true "hardware manual" any more. When you select manual mode the main control channels go into the 1280 chip and are passed right back to the output pins. If the mux chip is selected to manual then its just like the APM isn't even there.
Any how, you don't need this resistor. And the MUX on the schematic is connected to the 328 chip. It's just not shown very well. I checked it out with a meter once just to be sure.
Here is a high res picture I just took for you....