OK. So it might be compatibility problem of microsd card.
Surprised that you kept upgrading cart reader. If you are considering about upgrading your cart reader again, please let me share my wish list. It’s just my humble opinion though.
Would you please add screw holes on all 4 corner of board? Currently, holes are only on 2 corner of board. Other side of board only have holes on Arduino. I want to tightly attach PCB board on nice case using screws on all 4 corner of board.
Current schematic of SD connector is
GND 3V3 VCC PB0 PB2 PB 1 PB3 GND
Would you please add 5V constant(Not 5V/3.3V switchable) to SD connected?
GND 3V3 VCC PB0 PB2 PB 1 PB3 GND 5V
This will add compatibility to microsd module without removing 3.3V generator on microsd module.
Current schematics of adafruit clock gen connector is
VIN GND SDA SCL CLK2 CLK1 CLK0
Would you please add 3.3V constant(Not 5V/3.3V switchable)?
For example,
VIN GND SDA SCL CLK2 CLK1 CLK0 3.3V
This will add compatibility of simple I2C one way level converter and AE-Si5351A-B clock generator. You can also use these two modules sold in Japan too.
http://akizukidenshi.com/catalog/g/gM-05452/
http://akizukidenshi.com/catalog/g/gK-10679/