GPIO[2] not working as GPIO Input line

I am using Digi Connect ME® 9210 Evaluation board and the module.

I am trying to use GPIO[1] and GPIO[2] as the input line.

when i read the config Register A090_2000 using memwatch utility below are the output.

memwatch -r -w -a 0xA0902000

0xa0902000: 0x18080818

Some how GPIO[1] is configured as Ext init 0 and GPIO[2] is configured as EXT Int 1.

If i forcibly change the Register to work as input line with below command
/ # memwatch -x -w -a 0xA0902000 -d 0x18181818
/ # memwatch -r -a 0xA0902000

0xa0902000: 0x18080818 / #

Then after some time register value gets changed and sometime does not change at all.

Interesting thing is even with this configuration GPIO[1] works perfectly fine as input line
and not GPIO[2].

Highly appreciated the help from Digi to fix the issue.

is your SW3 set to GPIO? (GPIO Switch Bank 1, SW3)
Is your serial port configured to 2-wire? (TX and RX only)
ME9210 HRM can be confusing - GPIO-2 is not the same as GPIO[2].
GPIO-2 is pin 11 on module connector SW3-2 and P7-3
GPIO[2] is pin 12 on module connector SW3-3 and P7-5
Please make sure you are looking at the right pin