[Alan Anderson]

The problem is simple. When autonomous mode begins, all inputs from the OI are set to their neutral/off state. So neither trig_fwd nor trig_rev will be active when you read them the first time after the autonomous mode flag is set.

Fortunately, the solution too is simple. Instead of always calling Process_Data_From_Master_uP(), inside main(), only call it if you're not in autonomous mode. Make it the else clause of your if (autonomous_mode) statement. Make position a global (or static local) variable so you can use it later.