Eagle Ver 9.6
PCB_GCODE ver 3.6.3
Repeatable: Yes.
Requesting drill only:

First hole is OK, subsequent holes use the "Spot Drill" depth. This is a snippet from drill file.

Workaround: Make the "Spot Drill" depth the same as "Drill Depth". And don't forget to return to correct value for "Spotting" while requesting Outlines.
Regards, M.