In cutting parameters --> Containment turn on "Check Tool above Ball". I still notice that the tool holder is interfering with the check surfaces though. A bit more investigation is needed. Maybe by the GTAC team.
In the check geometry, have you checked the topology dialog for the face vectors?
Make sure to unify then face vectors and point them into the right direction.
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I did do that. I also thicken the surface to make a solid and added the solid as check. Still same issue. Not sure what is happeneing.