There are two ways to interpret the post:
1) You have a modifier volume that has a hole in it. The slicer is making the hole with the expected number of perimeters but making what you percieve as extra perimeters where the modifier volume interfaces with the rest of the part.
This is normal behavior. Modifiers essentially turn one part into two parts, so at the interface of the modifier and the rest of the part, you will have a [set of] perimeter(s) for the modifier and a [set of] perimeter(s) for the volume that is not included in the modifier, subject to the available space. It would be nice to have the functionality to select which parts, if any, have perimeters generated where multiple parts or modifiers meet, but I am not sure what would be involved in making that happen as far as the code goes.
2) When you change the modifier settings, it changes the whole part.
I would suspect you're not changing what you think you're changing. The top of the Settings window has the Object and then the individual STLs that comprise it. Even immediately after you've just added an additional Part or Modifier, the default selection is the entire Object. To edit only one part or modifier, you have to click on that Part or Modifier in that section at the top of the Settings window. The part or modifier will turn green in the picture on the right and the presentation of the settings at the bottom will change to those settings unique to the Part or Modifier you're editing at the time. Settings for a Part or Modifier override settings for an Object, which in turn override your baseline Profile settings.
If neither of these describes your circumstance, screenshots would help.
