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Using 6602 to measure multiple position encoders

I am trying to use the 6602 timer/counter to measure two positions that come from quadrature encoders. Currently, I have counter 0 measuring one and counter 1 measuring the other. Whichever encoder is connected to counter one is counted correctly. But the other encoder (connected to counter 1, or any other counter) is only counted correctly when position is positive. When position is negative, the counting is unpredictable and incorrect. Has anyone set up something like this before?
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Try connecting the encoder that won't count backwards to counter 0, which you know works. Also, try connecting the encoder that works to counter 1. Doing this simple test will prove whether counter 0 is good and all the others are bad, or whether you simply have one bad encoder.

Regards,
Justin Britten
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