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Have you tried a flip-flop yet? The MPGuino uses a polling strategy to watch the VSS input, meaning it only checks the status of the input at regular intervals. If a pulse from your circuit starts and ends before that interval comes around in code execution, the MPGuino will miss the pulse. The shorter the pulse, the easier it is for the code to miss it. A flip-flop doesn't have any such limitation and will convert the signal to a 1/2 frequency, 50% duty cycle square wave, very much like a standard switching VSS.
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