In the US we would say: He wasn't too happy when I came back a minute later with a box of jawbreakers.

the first and last sentence could be used because it says same meaning. the first sentence is more casual to hear.

Number 2 doesn't sound quite right. Numbers 1 & 3 are both fine but I would use number 1 and I think most other English native speakers would also.

Your comment is easy for me to understand:) Thank you Joellen.

To my ear, either the first or the third ("a minute later" or "after a minute"). The second option would absolutely be understood, but it changes the tense to present for a moment, which jars the ear. I think "a minute later" would be most common and "after a minute" is more formal, perhaps how you'd do it in writing. Hope this helps! Happy learning!