Views:
Some users see a problem where Autodrill will create a duplicate cutter for every hole after applying a sequence.  There is a preference that controls this called "Cutters_Merging_Rules"  The preference is located in Tools>Preferences>NC>Cutters_Merging_Rules and you have two options, Strict Compare and Flexible compare.  Switching this preference to flexible compare will prevent duplicate cutters from being created.
Some more info:

Strict Compare:
This is the default option.  When comparing cutters, set strict conditions for considering if the cutters are the same. For this option, ALL the geometrical parameters for the compared cutters must be identical for the cutters to be considered the same.  When this option is selected, all the other options in the dialog are grayed out.
Flexible Compare:
When comparing cutters, set flexible conditions for considering if the cutters are the same. For this option, the following options are available:
 Same Cutter when Cut Length is......To compare the cut length of the cutters, set the relevant option from the adjacent dropdown list.
 Same Cutter when Clear Length is.....To compare the clear length of the cutters, set the relevant option from the adjacent dropdown list.
 Same Cutter when Shank Free Length is....To compare the shank free length of the cutters, set the relevant option from the adjacent dropdown list.

The following dropdown list of options appears adjacent to the above options:
Different...Do not check the relevant cutter value.
Similar.....Compare the relevant cutter values.
If the deviation is 10% or less, then the values are considered the same.
If the deviation is greater than 10%, the values are considered to be different.
Identical....Compare the relevant cutter values. The values must be identical for the cutters to be considered the same.

In addition, the following holder comparison options are displayed:

Compare Holder Existence    When selected, check if the compared cutters have holders.
Compare Holder Name    When selected, check if the holder names are the same.
Compare Holder Shape    When selected, check if the holder shapes are the same.
These holder comparison parameters are considered independently.