I do not think it is about words. "You're welcome", as far as words go, is perfectly adequate, as has been suggested by posters above. But what about the body language, non-verbal cues, those things? Did you give him a broad smile when you said "you're welcome"? You wrote that you have trouble with social cues and with that you might also have some uneasiness around using non-verbal cues yourself to communicate with others.

Edited. Thought more about it. Maybe your words lacked a bit of emphasis. How about, next time, "Oh, you are MOST welcome!" with a broad smile? That should do the trick.