Weird deviation when extruding vertexes I banged my head yesterday, thinking my modeling was sloppy, but now I see the problem is somewhere else.

Take a look at the picture: 

What I did: simply extrude the top-left vertex to the bottom-right vertex of the cube, using the Snap during transform option, set to snap to vertexes.

In every case, there is a deviation of sorts and will happen on one axis (always the third axis, which should always stay at 0, but it deviates instead).

Does anybody know what's causing this issue and how to fix it?

EDIT: If I wanted to simply connect those verts, I could have done it just as easily by selecting them both and press "F" to create an edge. That is not what I wanted to do.

What I want to do: basically, by extruding vertices to other ones using the Snap feature, I was measuring if there were deviations in my mesh geometry, removing those extrusions after (with Ctrl-Z). The Extrude feature can easily be used as a measurement tool like that - even extrude a face toward a desired edge or vertex, to check how it sits in correlation to the face being extruded.

But with those deviations that happen even on the basic starting cube, how in the world can I use the Snap-to feature when it produces such deviations?
Try this - don't snap to anything.  Get into Ortho view mode so you're looking flat at the side to be extruded, extrude one vertice only a small distance in the axis that will take it along top edge.  Then press G and move your mouse down so the loose vertice is near but not touching the bottom right vertice.  

Highlite the loose vertice, and with shift held, highlite the 2nd vertice at the corner, press ALT-M and select "first to Last" or similar, to "marry them". (my term)

If that doesn't deform the cube's shape, do the same with the other side.  Round it all off by removing any doubles.