The PP is old technology that has been optimised over the long years it has been on the go, almost from the beginning of PC's I would think, and it is not known to suffer from noise issues too much. USB on the other hand can be problematic and it can vary from computer to computer.
Differential signals have an opposite for every signal, for example you would have a Step+ and a Step- and Dir+ and Dir-, this helps cancel out noise and makes things very noise immune, same with encoder signals, instead of having just A and B you would have A+ A- B+ B-.
To use differential signals either your hardware has to support it or you have to convert yourself with line drivers and receivers. Likely that would not solve your issues however as it iis USB problems you seem to be having, you could possibly try carefully cutting away the shield from one end of the USB cable to see if that helps, it did help some when using the USB SS.
Hood