EDIT: over on the #reprap irc Rhys-jones and a few other helpful folks figured this out for me. Since the endstops aren't working on my machine yet, the 0,0,0 position was based on wherever it was when it started up. I guess the x and y were similar to that same position, but the z wasn't. The fix was to add "G92 X0 Y0 Z0;" to the beginning of the gcode. That sets the current position to 0,0,0 on the printer. This can be done in the Start/End Gcode tab in Slic3r. Thanks again all who helped! /EDIT
This is my prusa reprap showing a strange z axis behavior using the sprinter firmware. Machine will jog correctly through pronterface. when it encounters the first .4mm z move it ends up moving significantly farther. It ended up moving around 1 cm.
This is the code for that abrupt z move "G1 Z0.400 F7800.000"
at the end of the video you see it begin the second layer, and it moves the correct amount! This is the code for that z move "G1 Z0.800 F7800.000"
I am very confused.
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