NI9401 unable to read digital pulses generated by encoder in FPGA programming mode

Hi all,

I am stuck and definitely use your help.

I am using NI 9401 on cRIO-9049 to read digital pulses generated by differential encoder. As 9401 is single ended TTL, I have connected only A and B signals (A- and B- are open). I am going to relace this module by NI9411 later. But for now, I have get this working.

I want to read pulses on FPGA using FPGA IO Node. I have connected encoder pin A and B to module's pin DIO5 and DIO6. This is how my chassis look like:

When I run FPGA  vi, I can't read any data from these encoder pins. But if I go to NI MAX and run test panel by changing programming mode to 'Real Time DAQmx' while FPGA VI still running, I can see FPGA VI gets the pulses from encoder. 

Can someone please help me to figure out what might be the reason for this behavior?

Thank you in advance.

Ashwini A Pandit