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SMARTRF06EBK: CC2538 Port A Pins not working as configured with zigbee

Part Number: SMARTRF06EBK
Other Parts Discussed in Thread: CC2538, , Z-STACK

Hello,

I am configuring PA3 pin as SSI clock and PA0 pin as gpio interrupt pin on my smartRF06 evaluation board. 

When my code run initialization part SPI works with PA3 as clock but after that when code runs task the sensor data is not read on SPI as i can see no clock on logic analyzer.

There must be change in PA3 pin functionality after my SPI configuration as it is connected to select button pin on board.

But when i change the pin PA3 to any other pin(example PB2) i can see the clock and SPI is working properly throughout . 

what can be the issue, as i tried removing the jumpers still not working for me.

Thank you