Update Stencil Master BaseIDs
Warning - this is a very dangerous feature - only use it if you know what you are doing!
If you create new master shapes you may need to change the shape's BaseID value, every master should have a different value, but this can only be changed programmatically. It appears to be very poorly documented.
Ensure only one Visio document is open, open the stencil you wish to update, then use the utility to change the BaseID values. When you create a new shape put that shape into it's own stencil initially and update the master's BaseID in that stencil, then move the new shape into its destination stencil. You only need to do this once per master.