I was happily (!?!) putting in the rake mouldings for the gambrels on Vassos. On the sixth one, the outer rake failed to subtract from the steep roof of the gambrel. All the others had worked. Imagine my joy when I saw that all five previous subtractions at the same condition had also failed.
The "solution" is to slightly change the edge angle of the upper roof edge. In my case, the angle of the edge when mitered to the upper roof was 74.3651º. I rounded up to the nearest hundredth of a degree, to 74.3700º. To keep the section through the miter looking presentable, I had to change the adjacent edge angle of the upper roof.
Over time I have have seen these subtractions continue to deteriorate, and I have to change the angles again. It's a pain, but there is no other way to model complex rakes.
Update: This issue is greatly improved in 10 and in the later patches of 9.