Yep, it sounds like you're not flaring quite enough so you want to follow the recommendation that others have already given. Just enough flare that the bullet will sit atop the case.
But since this started occurring after 2500 rounds loaded, I would check the instructions to make sure the shell plate is set as it should be to keep the cases centered as JSG mentioned as well making sure you're getting enough flare.
I don't know how you various progressive loaders are doing it, but if I were loading on a progressive, I would seat and crimp in 2 separate operations, Especially with a 5 station progressive.