Ok, luckily setROM_GBA() is only a small function so finding the bug in there shouldn't be too hard. 
So as a first try I would just test if changing the order of the operations fixes the issue.
Could you please change it like so and try again, the stuff we changed in my previous posts needs to be reverted to stock again ofc:
void setROM_GBA() {
// Set Control Pins to Output CS_SRAM(PH0) CS_ROM(PH3) WR(PH5) RD(PH6)
// CLK is N/C and IRQ is conected to GND inside the cartridge
DDRH |= (1 << 0) | (1 << 3) | (1 << 5) | (1 << 6);
// Output a high signal on CS_SRAM(PH0) CS_ROM(PH3) WR(PH5) RD(PH6)
// At power-on all the control lines are high/disabled
PORTH |= (1 << 0) | (1 << 3) | (1 << 5) | (1 << 6);// Set address/data pins to OUTPUT
// AD0-AD7
DDRF = 0xFF;
// AD8-AD15
DDRK = 0xFF;
// AD16-AD23
DDRC = 0xFF;delay(500);
}