JM1754, if I understand correctly something changed recently and before that change you had no issues. This seems to be the switch to a FL "type" die (whether type-S or otherwise). You've already determined that you aren't getting shoulder bump.
Lots of good input on this thread. You are correct to move to partial full length sizing (i.e. shoulder bump) as you can only neck size for "so long", however long that will be.
As you FL size you squeeze the case and the shoulder actually initially moves forward, until the die makes full contact with the shoulder and then starts moving the shoulder back. If you cannot screw the die into the press deep enough you will be unable to achieve this. So yes, the answer is either taking down the top of the shellholder or taking material off the bottom of the die. The last time I encountered this the latter was my solution as I needed to load on a progressive so taking down the shellholder was not an option. Pretty sure either of these, allowing for a 2 or 3 thou shoulder bump will fix you up.