Safe z after each cut

Why does the Z-axis go back to the safety z-height after some passes, but not others of the same type?

EX: I am using the cabinet maker app in Easel Pro. 3 of the 48 holes I put in for shelf pins cut exactly as expected. The 45 others did a plunge cut, back up to the 1IN safety z height set, and plunged again. Each hole took 3 plunges, and took an extraordinarily long time to cut the holes.