To anyone whos on windows, if you rename "application.py" to application.pyw, Python won't launch the blank command prompt window before launching the GUI.
(though you will also have to modify the startup script - i already did anyway.)
mine now looks like this:
@echo off
set PYTHONPATH=%PYTHONPATH%;.\;.\ui
..\application.pyw

Also, the setx command in the format setx PYTHONPATH %PYTHONPATH%;.\;.\ui (or whatever the proper paths are for you, sets the path in the REGISTRY) so you dont have to keep setting it everytime.