I have the exact same issue
Sorry to bring up an old thread, but I was wondering Hooligan, what was the final answer?
I have a Lyman Orange crusher press, and experience the exact same over-travel you described.
When setting my RCBS depriming/decapping die, I have to watch when the ram is at its highest point, hold it there, then screw down the die to touch the shell holder.
Problem with this press is if I were to let the arm go completely down. The ram rises to its highest point when the arm is about 3/4 of the way down. If I were to let the arm go all the way down, then the ram drops a bit.
I read the Lyman owners manual, and it speaks of a positive stop, I have yet to find this mythical stop.