Sorry about the late response. I have connected my controller via a cable and am not using DS4windows or anything like that. I'm using windows 7 home.
Hmm, I tried it on serveral PC's but I was not able to reproduce this. The d-pad (and the stick) work on all PC's with my DS4. Also not using any additional software. Maybe you can try it on a different PC and see if it works there? Or try connecting by bluetooth?