Navixer, your individual translations are correct, but the way you put them together is not. Fadelm0 is right. The literal translation is "pleasantly you came" (as in, "you came to me today in a pleasant mood"), not "it's nice that you came". So it's more of an observation (you are happy today, I see) rather than a personal statement (i am happy that you came).
To be honest, it doesn't really matter what the literal translation is, because it's simply an established phrase. Nobody thinks twice about who is the happy one. :) We're just glad somebody came. :D