Hi @garbagematt ,
Most common cause of scale or position shifts is improper import procedure.
When a mesh is imported into ZBrush with the Import function, it is scaled and centered to work in the program. The mesh may be difficult or impossible to work with if this didn’t happen. The values required to restore the original scale and offset of the mesh are recorded in Tool> Export. Under most circumstances this menu should have zero values active when importing any mesh. If it has zero values, then the mesh is centered and scaled and the unique values required to restore the mesh recorded in that menu.
Most problems arise when there are non-zero values in that menu at the time a mesh is imported. If any other tool is active that has non-zero values in the Tool> Export menu, the incoming mesh inherits those values. However those values usually aren’t intended for that mesh.
The only time you want to do this is when you are replacing a mesh of the same size, for instance to update UVs. In most other cases this is going to cause a scale or offset shift for your mesh that may not be apparent until you export it and those values are applied. In ZBrush the mesh will seem properly centered and scaled.
To sum up, always make sure to select the default polymesh 3D star as an import target before importing any mesh. This is solely because it has zero values in the Tool> Export menu and you can be assured of a clean slate. Don’t import a mesh with any other tool active in the program unless you a re attempting to update a specific mesh.
If this does not explain your issue, then something else is at work. Check the import and export settings in your target program very carefully.