Unable to Scan device chain. Can't scan JTAG chain

Hi,

I have a custom board with Arria II GX device that gets programmed from EPCS64 device.

I had built two prototypes earlier(with commercial grade device) and I was able to program the flash using JIC file successfully. On second set of 3 prototypes(design not changed, but FPGA changed to industrial grade), When I tried to detect JTAG chain, I get an error message that it is unable to scan device chain.

Options tried but with no succcess:

1) Changed USB blaster cable

2) Altera programmer tool PC

3) Drivers were reinstalled and checked

4) All resistors/mode pins checked

Observed the following on oscilloscope:

1) TCK comes at 5MHz till I get error. After error is displayed, no TCK comes

2) TMS is high initially, Goes low and then to high again.

Can anyone suggest any options to solve this issue?

Thanks in advance.