SE,CLEAR should be set larger than SE,SBAK. Units are always millimetres regardless of working units. After each point backs of the probe should move to the clearance circle and then make intermediate moves to the next point along the clearance circle.
It really shouldn't have a problem moving through a 1/2" gap unless the boss is grossly out of position.
If this is of no help please indicate, CMES version, probe dia., boss dia., stud dia.

Duncan Mackenzie
duncan@lk-cmm.com