I'm using a bare 1280 board for HIL simulation, with an FTDI cable plugged into the serial port instead of an Oilpan.
Attempts to download from the Firmware tab results in "Can't Detect Your APM Version. Please Check your Cabling".
HIL code fits and works (at least with X-Plane) if I download using the Arduino IDE.
I'm having issues getting the Aerosim interface to work and wanted to try the "release version".
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the only reason i can think this is ahppening is the dtr line on the ftdi isnt pulling ti down well enough, as what you describe shoudl work just fine