Printing goes beyond Z endstop limit

Makerfarm Pegasus 10", with lead screw and metal upgrades
RAMPS 1.4 on Marlin

I'm brand new to 3D printing, and while I've learned a lot this month, and continue to make progress, there is something I am experiencing that puzzles me. I'm not sure if this is working as designed, or if something wrong is happening.

My understanding is that the end stop will determine where the 0 point is on the axis. The Z end stop is located at the bottom, so that when it is hit, that means that I am at 0 Z, correct? But to be able for me to print correctly, I have to raise my endstop higher that I would expect, so that when I hit the end stop during auto home, the nozzle appears to be 1-2mm away from the print surface. This is because when I start a print, it autohomes, and then it proceeds to move down further. This happens in when using both slic3r and S3D. I believe my Z starting point in my gcode is usually around .4mm.

When I do manual bed leveling, my LCD display reports the endstop at being 4.00mm. To level the bed, my points usually end up around 1.5mm to 2.5mm, depending on where my bed is at during all the different times I have leveled the bed over this month.

I've realized recently that I've needed to bed level a lot lately, and I think it's because my endstop is not being reliable. Perhaps it's because the Z motor is pushing down on the end stop so hard, beyond the end stop point itself, that it's pushing it further down my V slot?

Are prints supposed to start slightly beyond the end stop, and I just need to do a better job at securing down the Z end stop so I can't be moved? Or would that just be fighting the symptom, and I need to knock out the actual issue, which would be the Z axis going 1-2mm beyond its endstop?

An end stop is a end stop, when the Z axis moves down and hits the min_ z endstop the nozzle tip should be a paper thickness from the bed, this is now at Z0, the nozzle should not go any lower than this.

If you are slicing the files for printing yourself, then check that you don't have a Z offset set in the slicer. If you got the files as gcode from somewhere else, then get the STL files and slice them yourself. As obewan says if you have set your Z limit switch correctly then the head should home to a level the thickness of a piece of paper above the bed printing surface.

The offsets are never negative. For example, here is what my GCODE would look like when it goes to its starting position:

G1 Z0.200 F1002
; layer 1, Z = 0.2

So yeah, it's what I thought; my z endstop should be at the point of paper thickness above the surface. But instead, I have to be over 1mm above it, because without fail, the printer is going beyond the endstop.