We are having trouble loading the code, and keep getting errors. We have a 3.3V (3 cell 11.1V) battery which we believe should be correct, but for some reason cannot load the code properly. All our hardware appears to be connected properly.
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APM startup sequence is a little ambiguous so I posted a more detailed one for others.
AP seems to have a different sequence dependent on the software loaded so read the manual and have a look for what it should be.
As for loading code I can only comment on the APM (what I have) and the Tx and Rx LEDs flash while the sketch is loading and when loaded it does the startup light sequence.
If you are getting errors I would put money on it being your IDE setup and not the AP setup. Given there are many people flying without problem its more than likely something in the IDE is gone squinky. Make sure you set it up exactly as in the manual and it will work. The sketchbook folder being set wrong is one of the common ones.
I presume you are powering the board through an ESC. You can't power it directly from a battery unless you switch the BATT solder jumper (and even then, 11.1v is too much). All this is covered in the manual.