The prototype works well but the biggest handicap is the way FT232 chip reacts to environmental noises. It can crash and reset the USB connection even with minimal noise radiated from a near-by device such as an adapter being plugged in and out an outlet.
The cases where incorrect design (filtering, decoupling etc) or layout (skimping on layers, no concern for trace coupling etc) has been balmed on a chip are too numerous to count.

BTW 'prototype' is your prototype a proper PCB. If it is a rats nest or some "prototyping board", there, very likely is the reason.

Erik