Karyn could have been smart about this and just wish to know why her most recent wish had changed her into a boy, but no, that's not what happened. She was so weirded out by her change from female to male that she instead said "I wish I was a girl."
Now, the previous wish was not for her to be a boy. That was just a side-effect of the wish. So there was nothing there that couldn't be reversed, for her. The wish did exactly what she wanted, causing her to not only become female again, but also get back the long blonde hair and big boobs she had before she had become a boy. She still wasn't too wild about the hair and the boobs, but at least she was back to being female again.
But thanks to the previous wish, Jon was gay and in love with Karyn/Karl. Well, if Karyn was female, then Jon couldn't be gay and in love with her at the same time. Not to mention that part of that previous wish was for Jon to have a crush on "one of the other guys at school". So to work around this apparent contradiction, the stone made it so that Jon was now a girl version of himself named Jenny, but also bisexual, so still "gay" towards other girls, but straight towards guys, including the guy she now had a crush on ... whoever that was.
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Back at her house, Jenny just couldn't stop thinking about the guy she had a crush on. It distracted her so much that she couldn't concentrate on finishing her homework. Normally, she was only interested in other girls, but this one guy - there was just something about him that made her fall for him.
So who was this perfect guy that Jenny wanted so badly?