After Effects CC slant effect crops artwork
Depending on how you imported it, it is possible that it ended up nested as a nested composition or smart object.  If you applied the effect to the outer object but then dragged it within the inner object, you could end up dragging it off the edge of the outer object which would produce the result you are experiencing.

Effectively, you would have an outer object that is tilted and an inner object that is going off the edge of the outer.  Thus, the outer object displays only the half of the object you see and then the skew gets applied (which makes the otherwise vertical clipping to be angled.)

That's the only thing that occurs to me as a possible cause.

Even if that isn't it, a work around might be to put the original graphic in a composition and then apply the effect to the composition instead and then move the composition as you need.  This would probably work around whatever issue you are having here.