Discrepancy between GPIO Config Tool and Pinout Designer/Silkscreen on Apalis Eval board

I ran the GPIO Config Tool on an Apalis SoM connected to an Apalis eval board(v1.1), and proceeded to add in the initialization of GPIO_1 thru GPIO_6 in my code. However, found that the mouse and keyboard were now inoperable.
Upon further review via the eval board schematic, and the pinout designer, found that the SODIMM values reported by the config tool do not seem to agree with the SODIMM values that the pinout designer and silkscreen indicate.

See below:
alt text

Eval/Loc shows X4, ended up using X2, and removing X3 in between X2 and X4.

Is there an issue with what GPIO Config Tool reports and the Silkscreen data?

What OS and exact versions of things are you talking about?

WinCE7 I see reference to Colibri in the description of the Windows CE Tools section, with Apalis iMX6 with nothing indicating what level of support. My eval board is Apalis iMX6.

Can you please provide link to this information. Also where did you download GPIO tool? This is correct tool for iMX6 iMX6 GPIO tool