I'm taking a stab at it and guessing that the initial extrusion that the part's based on was double-sided. You've used a mix and match of construction methods and I think that that's introduced some workplane confusion. When you've sliced the part and got your unexpected result, select the bottom item in the part tree and choose "edit content". Move the extrusion half its thickness in the Y axis, click the green tick in the part tree palette header, the drawing window reverts to the part view and the part has rebuilt with the correct result.
An interesting (or not. YMMV) thing to try is, instead of slicing, create a box that encloses the section of the part that you want to keep and intersect it with the part. This is a little more efficient than two slices and deleting the offcuts, but aside from that, the intersection is as you'd expect the sliced part to be. Don't ask me why, I got nuttin'.