I think that Bowser deliberately told Bowser jr. that Peach was his mom so that Bowser jr. would aid him in kidnapping her. It makes sense to me. I would do it.
And peach is definitely not bowser jr.'s biological mother. Bowser just needs someone to do the dishes and clean the castle.
Also look at the new super Mario bros for DS. Bowser jr. kidnaps peach there too.