Comment 3 for bug 1669360

I thinks this behavior is result of how Sodipodi treated the coordinate system. Inkscape inherited this 'cartesian coordinates' where the Y axis is upward in contrast to SVG standard and other software where Y axis is downward.

You can read more about this 'feature' here: https://bugs.launchpad.net/inkscape/+bug/170049

If you take a closer look at coordinates of your "zero-located" object you could find in XML Editor that the Y-coordinate is not actually equal to zero. And this is why your objects "jump".

What about dimmed Y-scale — it is used for non-uniform document scaling and normally shouldn't be used. I personally have never seen documents like that. Even if you set Y-scale to -1 it will not help you to avoid "jumping" as the origin of a document is misplaced in SVG terms.

I recommend you to setup document units before doing any graphics.