Hello @PinkMan, please accept my apologies for being so long with the response. The described behavior is a bug, we are going to fix it in one of the next Document Server versions. We will inform you when the solution is available.
Method UpdateAllTOC does not work properly when is fired inside the document creation script for DocBuilder, but if you execute the creation script without oDocument.UpdateAllTOC(false); and then execute separately oDocument.UpdateAllTOC(false); - the numbering will get updated.