Wow, you spent a of effort on your Uzebox there! What is your programmer brand/model? I never used Avrdude but if you have a programmer that is compatible with an AVRISP MKII like this one on ali express, you can use Atmel's Studio or the atprogram.exe command line tool to program everything in a way that I know the reliability.
Topics regarding the Uzebox hardware/AVCore/BaseBoard (i.e: PCB, resistors, connectors, part list, schematics, hardware issues, etc.) should go here.
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