Certainly in the last Candidate 6.8.18211 (but one of my Clients states that this Bug is present since the beginning of Version 6) using MakeHole and pressing Enter immediately after selecting Curves and Polysurface no longer produces a through hole as it should.
I, too, ran into this problem. A sort of work around was to raise the object above the cutting plane and cut holes all the way thru from the bottom. Then, I lowered the object back down to it’s original location.
But, I couldn’t make a hole to some designated depth no matter where the solid was.