Jon never would have wished it normally. But it was a stable time loop. He made a wish which would, much later, force him to travel back in time and make the very same wish, keeping the time loop going. And it also forced him to make the second wish:
"I wish that Jessica would slowly transform into a boy for over the next week. I wish that there wouldn't be a lot of publicity over it and people would think it's strange, but forget that it's impossible. Also, I wish that Jessica would get used to being a boy, but only for the next three years."
That explained it! Three years ago, Jon had been a girl, Jessica. For some reason, she had transformed into a boy and had to change her name to Jon. Now that Jon thought about it, it was an utterly impossible thing to happen--people don't just change sex, after all. But he had never noticed it. Even people like Karyn who knew him from when he had been Jessica didn't realize how impossible it was.
He couldn't even blame anyone for the wish, since it was a time loop--the loop was its own cause; he just made the wish because he made a wish which happened because of itself.
At least some of it had ended. The wish only said that Jessica would be used to being a boy for three years. Jon could already find himself remembering bras and periods with fondness. Well, not the periods. But could he change back? He suspected that the transform was permanent, but on the other hand transforming doesn't mean you can't transform back.
Jon had to talk this over with Karyn. "I wish I'm back in the future again."
"So where did you go and what did you do?" asked Karyn.
"How long was I gone?"
"Five minutes, my time."
"That's all? Anyway, here's the story...."
