I don't think you mentioned if your press is single stage or progressive...
Before modifying the die...
Make sure that your shell holder (if single stage press) is clean and that your case is sliding fully into the shell holder. If it is not, when the ram raises, it will not be properly aligned with the die.
If progressive, and for some reason it does not index correctly, it could also be misaligned and not go into the die properly (but all stations may also have issues)
I would definitely do an inspection on all dies, reset them up and go slow to see if it duplicates and you can isolate it.