I'm confused because, etymologically, there's no difference between the two statements. I see them as two parts of a whole, in fact: "it was no problem; you're welcome to ask again." An "any time" can also show up in there.
Except that for some favors, it's not true that "It was not problem", even if it is true that "you're welcome to ask again". In these cases, I use "you're welcome".
