How are the ATMega pins labelled ?
The pins on the ATMega128 are PC0 thru PC7. The silkscreen labels on the component side of the board are the header pin numbers and are numbered 1 thru 8. This matches what’s in the schematic. The PC0 thru PC7 labels are on the bottom of the board. I’m guessing that you did what I did and assumed the the top label of three (3) corresponds to PC3, but in fact it’s the one labelled 4 on the top (and labelled PC3 on the bottom).