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I noticed that the MOD5441x Datasheet was updated 14 July 2017.
(I should have put this up before so that it could have been included in the latest release. Sorry for the delay.)

In the MOD5441x Datasheet, page 5, the definitions for pins J1-9 and J1-10 are reversed.
If you switch the pin numbers you'll have the correct definitions.

The definitions in "pinconstant.h" are correct:
J1[9]: device pin D1: FB_BE1; FB_TSIZ1; PortA1 GPIO
J1[10]: device pin F4: FB_BE0; FB_TSIZ0; PortA0 GPIO

(I believe I tested the hardware to verify, but if I'm wrong, I'm sure you'll let me know.)

Thanks for pointing that out. To put it another way, the header pin number, signal name, everything else is correct. It is just the CPU pin numbers that were swapped.