Alex,
I am living with this bug and getting the results I need. I ust have to check the gcode w/ ncviewer.com and often closing WAM and starting from scratch is the best solution.
I estimate I am getting gcode from WAM w/o certain holes about 40% of the time, even when following your guidance here.
Hopefully your team has a ticket for this w/ a near term fix.
Thanx again,
Jim