Unless you tell us if you are using Windows 10 or not, and if it's a laptop or desk top computer, what your vid card is, there too much guessing on what to tell you. All you had to do is unzip the no cd exe, go to your NR2003 root folder, move the game exe out, move this new one in, then just double click it to start the game. Why would you run the config exe....has nothing to do with the game exe.
Next thing to do is a fresh install, leave the old one installed, just name the new install different like Papyrus2, once installed don't change anything, see it it runs first (assuming you have the cd of course) If you downloaded the game, change out the game exe with the no cd exe then start the game.