Most likely your object is more than slanted, it's non-planar. If you hit 'w' in polygon mode the list will tell you if you have non-planar polygons. If you do, then mystery explained. Bools and stencils always get defuncitated by non-planar polys.
If you have non-planar polys then you either need to triple them first, then try it, or model the shape so it does not become non-planar in the first place.
If you don't have any non-planar polys then do what Mark said and post us a screen capture. And seek the advice of people smarter than me.
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