MCP3428 ADC Gain Errors
According to the datasheet it does indeed have a mux and a single PGA - as well as a single ADC.





I know that still doesn't tell you why the channels respond differently.

I thought it would be good to verify how the thing works before we go off chasing the wrong thing.

So, now we know it can't be a mismatch in gains on the PGAs because it only has one.

Can't be a mismatch between ADCs - again there's only one.

Might be some slight differences in the mux channels.

Might be some differences in the impedance of the circuit outside the chip - whatever signal you are feeding it.  

Might be something else entirely, but I sure don't know what.