Since the grammar in all is correct, I discuss the use of each.
"Don't make me miss you." a rarely heard instruction. "you" must be a charming, nice person. If I like the person, I will miss when the person is absent. "Don't make me miss you" is like saying "Don't make me like you much." It's a joke really.. Of course I want to like the person.
"You made me miss you" . I have said this. Imagine this conversation A "I missed you dear" B "Why do you miss me?" A "You made me miss you" .. A thinks B is so nice. A likes B, so if B is gone, A misses B.