What you are describing is not possible as a result of changing slicers, this must be an intermittent hardware issue.
The slicer has no knowledge of the hardware layout of your machine (other than the build volume and gantry dimensions; if properly configured), it just creates slices of the model you present which are found in the G-code file as Z movements. In case multiple Z steppers are used to move the X gantry, these are usually driven by a single driver, but if they are separately controlled, even in the G-code file the instruction would be to move up Z in total, not per stepper. It is the firmware of the 3D printer that translates this Z level in movement for your 3D printer based on the layout of the machine and the firmware settings.
The CraftWare G-code file does show some inconsistencies with respect to the Simplify3D file in that it does not use
G29 and has a too large first layer height of 0.45 mm (this is larger than you nozzle diameter of 0.40 mm, you should always limit that to about 75 % of your nozzle diameter).
For an X gantry to become unlevel/skew, there must be a mechanical issue that is causing it to miss steps/prevent advancing at one side. It is possible that one of the shafts or lead screws has some more friction than the other (generally it is not a good idea to grease the screws as dirt easily stick to the grease, a light oil may be better suited). This is not uncommon for Prusa i3 clones and is usually fixed by resettling the leadscrew nut by loosening and tightening the screws which attach the nut to the X gantry idler. It is unclear if this is your problem here with this specific machine.
To be fair, uneven displacement of any axis powered by 2 separate motors (driven by separate drivers) could be induced by the slicer when unrealistic high accelerations and incorrect hardware/electronic settings are employed.