One more thought... While I don't really plan on using the EEPROM saved values for my Auto Bed Level Correction matrix, I'm not opposed to putting that code into my firmware. I would just do a G29 every print and over ride the last saved value. Perhaps it makes sense for me to put that code into my firmware, and for you to cross your Configuration.h (and maybe Pins.h????) over to my code base.

If we did that.... I should be able to duplicate any problem you are seeing....