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Why does my linear encoder only read negative?

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I have a linear encoder I am trying to utilize with an NI cDAQ 9184 & 9401.  I basically used the linear encoder example I found here on the NI website, however, when I run the program I am finding that only measuring in one direction is the displacement reading accurate.  By that I mean when my encoder is moving upward (in actuality my fixture is moving down and the encoder is fixed) I am measuring displacement correctly, but when moving in the opposite direction I am way off.  I am not off a linear amount either, very different each time.  Sometimes when the movement first starts it almost seems like the device is resetting back to initial position (0") but I am clueless as to why.  Does anyone have any idea on how to rectify this situation?

I am fairly confident I have things wired correctly as this same encoder/setup reads correctly in MAX, see the second screen shot.


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