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TMS320F28379D: Launch Pad F28379D QEP issues

Part Number: TMS320F28379D
Other Parts Discussed in Thread: BOOSTXL-DRV8305EVM

I have issue as .

I use BOOSTXL-DRV8305EVM + Launch Pad F28379D combination. Everything works except the QFLG.IEL bit. I tried two encoders. Both of them did not work. I looked at the signals on the scope, and I can see that the index pulse is connected. (I have not checked the input to the IC, U2 on the Launch Pad).  I have a custom system based on F28377S, and this code works on it. That system also use GPIO 20, 21 and 99. GPIO99 is the index. I also checked two Launch Pad boards. Both of them have the same issue. I use proper ESD protection when I handle these boards. Can you please help. 

Thanks,

Dhammika