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When you input a signal from an external circuit, you have to make sure that you unify the ground pins in order to band the logic levels together, so you need to tie the ground of your external circuit with the ground of the DE1 board (you can take it from the GPIO header, I think it's pin number 12... check out the schematics).
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I've already done this. I only use the gpio pins for supply. The ground pin as well as the 5V output. For input I used different voltages between 1,5 V and 2,5 V (generated by using the 5 V) and another time a direct connection between an output pin and an input pin. I've also tried out different pins to check if perhaps one pin is defect, but it makes no difference.
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