Can't subtract an object all the way

[michael3]

When I try to subtract this small object, it will only do a half rotation; but the problem is, I didn't even adjust anything! The last pic shows what I was trying to subtract. I deleted the very large cylinder that I was subtracting from, and that fixed the problem. What could the problem have been with the other cylinder?

[JBorlaug]

Was the original a mirrored section? there is 3-4 ways to build this kind of a shaft. the single most common hassle I run into, is in the way upper left corner, to check the correct options for (entities,objects,distance,vectors etc.This program is so deep, it's easy to forget the 'details'!
Johnny