Slicer now reads all files in LPS coordinate system. Before Slicer-4.11, it expected STL files to be in RAS coordinate system by default. See more information about how to avoid RAS/LPS mismatch in the migration guide.
If there is no LPS/RAS issue but slight position and/or orientation differences then most likely that other software does not properly take into account image origin, spacing, or axis directions of the input volume.