I use a slightly different set of tools, but I've never encountered bullets being seated crookedly. I use a set of Lee dies plus a Lee Factory Crimp Die in a Redding T-7 press. I don't use the powder-through feature, but it is the same die. I use the same bullet. When I seat the bullet, I have the seating die set to just remove the belling to the case, but not crimp. The bullet is seated so that the case mouth is near the bottom edge of the crimp groove. I then rotate the turret and crimp with the FCD. The bullets go in straight and, as long as the cases are all close to the same length, everything works fine.
It is possible that I modified the seating stem on the Lee seating die--I've been using it for a long time and I don't remember. If I did, it was to keep the stem from making marks on the bullet, not to seat the bullets straight.
That doesn't answer your question or problem, I'm afraid, but it does indicate that I'm not having the same problem with some of the similar equipment...
CC Griff