There's a reason for this faulty behavior. When an object has a small modelling bug, the automatic correction features in ArchiCAD make it display correctly in 3D. But when it comes to cutting this slightly incorrect model, the cutting algorithm reveals the problem and it can't fix it.
All in all, this object has a modelling bug which I entered into our bugtracking records.
Thanks for highlighting the problem for us. I'm sorry about your inconvenience.
Regs,
Zsolt Táskai
ArchiCAD Development - GDL Team
AC13, AC14 and upwards...