I have had some issues with every NIB pin that I have bought. Sometimes it's a simple as adjusting a switch. Other times whole parts have had to be replaced. So I don't think this is common to just JJP. Stern has had some colossal misses when it comes to QC as well. Seems to happen with all of the companies.
I have a WOZ, bought it NIB from Larry at flipnout pinball. He drove 3 hrs to deliver, brought it in my house, we set it up and worked out any kinks in it. The only issues mine had was the ball trough was stuck and the crystal ball cable was loose. Took a couple of seconds to fix. I think I've had it for 7 months now with zero issues. When you are paying that amount for a machine and there is no discount I expect a little extra. I don't buy for one second that the distro are only making $500 on these games. That's why I went with a distributor that would deliver and set it up.
I realize that many of the early machines had lots of board troubles, that's why I try not to buy many games early on in production. When you buy early, especially from an company that is not proven you will likely have several problems to work through.