I would seat the bullet whereever it shoots the best. If that means using it as a single-shot, so be it. This is very common among longrange hunters and competition shooters as accuracy is the main concern. If you are not crazy about accuracy, then seat it to whatever functions flawlessly in the magazine.
Nickle cases are more rigid and therefore more difficult to bend. When you resize, the necks are made smaller and seating a bullet forces the neck back out and being in a nickle coated case, this is more difficult.
It is also possible that the neck on your resizing die is on the small side of the tolerance range, therefore making it even more difficult.
Kyle