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Quadrature Encoders and NI-MAX

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I am using the NI 6259 DAQ to read a quadrature encoder.  The datasheet for the 6259 states that any PFI designated channel can be used as a counter/timer; however, there are only two channels that seem to work.  When I set up one of the other PFI channels, the encoder read out on NI MAX changes from 0 to 36m, but nothing in between.  It appears to be set up exactly the same as with the two channels that work.  Any suggestions on what I could be missing?  Are not all PFI channels created equal?


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