I remember it taking a while for EB's production to catch up with demand, so during that period there may have been some folks who got their hands on the early JP's trying to milk a little extra money out of those who really REALLY wanted an EB JP.
I've had several of the JP's (a candy apple red 6, a mystic dream 6, and a carbon blue pearl 7), and they're great guitars for the money... EB's workmanship is top notch (I think they're some of the best bolt-ons you can get) and they play like butter. Personally, I find the tone of 'em a bit dark for my tastes... I actually prefer the tone of the Ibanez JPM's, of which I also had several over the years (a JPM1, two JPM2's, a JPM3, and two JPM90's).
--B