The gcode files have exactly the same z-coordinates in the file. Open the files in a text editor and take a look for yourself. The last layer is printed at z=20mm in both the v2 and v3 gcode files.
Since the gcode files from both versions are correct, this means that your printer is somehow interpreting the gcode files differently. As was noted above, a recent leapfrog firmware update apparently screwed up their steps/mm values, which would 100% cause the issue you are describing. Follow the suggestion in the post above to correct the mistake in the new leapfrog firmware.
