I did a bunch of tests yesterday.
I'll post the full results later.
Question: Is there anyone with this problem using a printer other than the Leapfrog Creatr?
Here is a quick overview of what I did find:
1) It's can't be G92 E0. Kisslicer uses that too and prints sliced with that and printed using S3D as the host come out fine.
2) It's not skipping steps due to speed. I ran some tests at very slow speeds and the part still had a huge skew in the Y+ direction (but in this case not in the x-axis). (Kisslicer parts printed at a lot faster speeds are okay.)
3) EMI seems highly unlikely since only slices done with S3D have the problem.
4) The skew problem follows the gcode file from S3D. Running the gcode from S3D using Repetier as the host are still skewed. Parts sliced with Kisslicer and using Repetier are fine.
5) The part I'm using (which I unfortunately can't post) is a small round part with "flanges" at the top and bottom. The flanges at the top and bottom print straight, but the center section is skewed. That seems to indicated that the geometry of the part is involved somehow. (The part was designed in SolidWorks.)
The elephant in the room of course is if there is a problem with the gcode (and the tests seem to support that) then why do they look okay in the previews of both S3D and Repetier?