Cannot use SCI-7 pins on DKS7G2 as GPIO

I have written a Custom (SPI Based) driver by configuring SCI-7 pins viz.  PA02(MOSI),PA03(MISO), PA04(SCLK),PA05(CS) as GPIO's. However what i observe is pins PA02 & PA03 does not toggle by gpio write/read API's, it is drwan to 3.3v constantly.

 

There is no problem with the other two pins. I checked the synergy generated files and all the pins seems to be configured as GPIO op/ip properly still why this must be happening?