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PXI-6602 and quadrature encoder

i have a PXI-6602 in slot 2. the 6602 has a TB or BNC 2121 accessory breakout. i have a linear encoder with channel A connected to PFI-39 (pin 2). i have channel B connected to PFI-37 (pin 40). not using Channel Z so not connected. i have connected the 2121 clock to PFI0, used as external clock input (set to 1000 hz). i can move the linear encoder and see pulses increase and decrease but can never get back to zero. for example, if i slide the carriage one direction and the count goes up. if i slide the carriage back to starting position but count does not go back to zero, lets say the count is 1000. if i slide the carriage back forward again, the count increases further than before. when i slide the carriage back to starting position, the count does not go back to zero and does not get close to 1000, lets say the count at zero position is 2100. as i keep sliding the carriage back and forth between the two points, the count at the two physical end points will continue to increase over each cycle.

can anyone tell me what's wrong?

the setup is for continuous samples, rate is 1000, samples per loop is 100.

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