Most intriguing! I don't have an answer, but here's some more discussion for thought...
At least to the precision you printed out, points 4 and 13 are identical, as are points 8 and 12, yet these vertices have not been merged. That is probably the cause of the behavior: the sequence of vertices looks like an ordinary outer loop to SketchUp. But why are they separate? And why did SketchUp gather them into a Face? Possibilities that come to mind:
- they differ in decimal places beyond what you printed but still larger than the merge vertices threshold of 0.001". I don't know what units you used, so can't tell. At full precision, there might be a tiny gap between these points.
- the merge vertices and geometry cleanup operation misfired (which would be a bug!)
- the intersect operation explicitly built these Faces that way (which would also be a bug!)
Regarding the randomness, do you get different results if you undo the operation and then redo it with the identical geometry? If this produces the same results but moving or changing the geometry in any way causes different results, it sounds like a computer arithmetic problem that varies depending on the exact values encountered (not that this observation gives you a clue what to do about it
.
One trick I've had work in some situations is to nest everything one extra level deep in a Group, do the work, and then explode that temporary Group when completed. This seems to trigger another round of geometry cleanup which may repair the flaws.