I just looked at your job file and it shows Ztop 0.000 for both operations Huh??
yes, that was the problem. Ztop was not being saved in the job file, and it was not being passed to the gcode generator. The same thing was happening to all 4 hole operations.
There is a bit of a problem on those ops. The Drill cycles do not have a parameter for Ztop, they always start at Z=0 Only the circle and circle pocket can have a non zero top.