Did you get it fixed? I've had problems with alignment for seating primers. Index pawl was adjusted properly, and I'd loosen the 2 screws that bolt the shell plate platform to the main shaft, try to hold it in place as I tightened those screws. Still wouldn't really fix it, and to be honest, I didn't find Dillon's alignment tool all that helpful. The trouble comes loading military .223 brass. I think it's just that maybe the primer pockets are not consistently in the center of the cases. I've learned how much pressure I can apply, without smashing the primer. If it's not going to go, I give the case a spin, and then normally the primer will seat (hence why I think it's maybe my brass... although I've tried lots of different head stamps, and all give me the same problem). After battling this for a while, they sent me a replacement shell plate platform, and that seemed to help some.
To try to alleviate the brass issue, I've been trying to swage it as much as possible...keeping the case support rod long enough that the case fits tightly into the swage maybe 60-70% of the time, and takes a light tap with a hammer or deburring of the flash hole to get the case to fit into the swage the other 30-40% of the time. I thought this method was working pretty well...not having to spin as many cases to get the primer to seat.... until I had a primer fall out of a round and jam up the lugs in my rifle at the local 3gun match this past weekend. So now I wonder if I'm over-swaging?? Never a dull moment....
What is it they say? If it was easy, everyone would do it?