Mortek,
Keithorr is basically correct. What OneCNC is doing is avoiding machining through the yellow pins, which is exactly what you would expect it to do, with its surface detection logic. When they are visible, then they are considered.
If the pins are not actually integral to this part, then blank them, as there is no danger of running into anything, because, in fact, they do not exist when the blue part is being machined.
That is my take on it, just by looking at what seems logical, but I've been fooled before by your models
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)