Are there any immediate differences between the two board? I cant visually see any, however the Mifare RFID reader and accompanying code i have been using doesnt work on the Genuine Arduino Mega R3 i have. On the genuino it still appears to power the mifare, but will not read so im feeling the difference would be in the I2C side.
The only suggestion I can make is to check the wiring; either bad contacts somewhere or maybe you swapped SDA and SCL. Note that I thought that the Mifare is an SPI device (I have no experience with them), but the same would apply.
Assuming that you power the Mifare from the the Mega, try to find the schematic for the Elegoo and compare the power circuit with that of the genuine one; there might be minor differences.
Saying I2C was a mistake, i have been using SPI, il chalk that up to brain fog after a day of debugging. I have verified all wiring, but as its a soldered custom pcb it would be hard to put in the wrong place. Ive since tested with a breadboard setup however and it works fine, so im definitely making a mistake somewhere. Thanks for your help, i think this thread can be considered solved as the issue is not with the boards being different.