If I had those marks, I would've got a pretty good mark on it. But I actually FAILED that assignment because THE PHYSICAL CD DISK WAS NOT LABELLED.
Sounds like a douche of a professor.
There area two things to think about here. You could talk to the professor, but it sounds like he is either an ass or dislikes you for some reason. I had a situation in my undergrad where I did work that was clearly had and shoulders above everyone else in the room and was constantly marked down because the professor didn't like me. And it was entirely mutual. He was a wishy washy pretentious jackass.
Anyway, on those projects where you feel you have been marked down unreasonably, are the things he is busting you on part of his grading rubric or grading criteria? If they aren't, and he is using it to bust you down you may have grounds to file an academic grievance. Most universities have a process for disputing grades and filling grievances.
It won't endear you to him, but if he isn't grading according to his own rules, or if there are no rules you may have solid grounds to dispute the grades.
Honestly, if your work is good it might be worth investigating. If your work is shoddy to begin with then you'll look like an ass when he has to regrade you, and gives you the same grade for poor work, not just poor labeling.
Grading is really designed to provide holistic feedback to students as a way to communicate how well you demonstrated your learning. But if labeling isn't part of the grade then he should back off.