When you load the file into Biesse works you must Optimise the machine program and set the “Optimise” options to “minimum time”.
This forces Biesse Works to see if the holes are lined up at 32mm and it should automatically use the drilling head.
Without optimisation the machine will drill one hole after the other.
If this doesn’t work it might be that the drilling head configuration of the machine has been changed and the drilling on from Polyboard that is lined up doesn’t match the head config that has been modified.