There was a hardware fault in the very early Pod GO units off the manufacturing line. It affected resistance in the input circuitry. It was resolved fairy quickly but it's possible that your older Pod Go unit has this fault and the later one does not. That could explain the difference. To be sure open a support ticket. If your old model is flawed Line 6 will repair it for free.
Having said that, the repair would make the older unit sound like the newer one, which is not what you want. Get advice from Line 6 while your support ticket is open.
And, of course, the issue could be something else. But start with this possibility.