In DSpace 3.x, whenever you mark an Item as "private" (whether during deposit or when editing the item), behind the scenes is it withdrawn from the system (i.e. in_archive=false).
This is problematic, as "private" and "withdrawn" do NOT mean the same thing. Withdrawn items are essentially removed from the system, and many of DSpace's tools (CheckSum checker, Curation Tasks, etc.) ignore any 'withdrawn' items.
However, a Private item is not being removed, it is just hidden from view/visibility. Therefore, it should still be processed by Curation Tasks, etc.
Therefore a private item should NOT be withdrawn. Instead a private item should have "discoverable=false" but "in_archive"=true.
Also see Andrea Bollini's good analysis of "private" vs. "withdrawn" items: