I suspect your problem has to do with confusion between signed and unsigned values. However since you haven't posted either your Arduino or your Python code I can do no more than guess.
This demo shows simple Python to Arduino communication
. It just uses bytes.
It is also fairly simple to directly send values for Arduino LONG and INT variables and if that is what you are interested in I can provide some demo code.
By the way these examples are in Python 2.7 - I don't use Python much and I haven't tried v3.