In my opinion, these differ somewhat. The phrasal verb "check up" has the meaning to investigate. It has the connotation that someone might have done something wrong. A suspicious wife or girlfriend might call to "check up" on a man who could be engaged in outside activities. On the other hand, if I call to check on someone, it is probably a friendly call to verify well-being. I might say, "Hello, Mother! I just called to check on you." I would not say, "Mother, I am calling to check up on you." My dear mother would never do anything wrong.