Attempts to use certain Zmodeler functions results in unintended vertices being merged
Sorry you’re having some trouble!
I have seen this sort of thing reported before in regard to the point welding, but it is almost always the result of a mesh being too large in the Zbrush worldspace. I know you said you have checked this, but let’s just make sure we’re on the same page.
For best results in Zbrush, a mesh should have a Tool> Geometry > Size XYZ slider value of approximately 2, give or take. The Unify function reduces it to this value. When this issue is reported, it very often turns out to be drastically larger than this value.
Double check the dimensions of your mesh in that menu. Understand that the QMesh function is supposed to weld points and is governed by snapping behavior, but the Polygon > Extrude function does not weld points under normal conditions.
If it is more or less properly sized and still produces the unintended point welding, I have no explanation for the reported behavior. You should submit the tool that can reproduce the issue to Pixologic Support.