I have tested plain VSD with the standard stencils and inserted Screentip = No problem after 10 minutes.
My VSD has macros and is also using a stencil with VBA.
That seems to make this break in Visio 2016.
A workaround I have found to work is that I to disable "Save AutoRecover information every XX minutes".
XX was set to 10

Why this happens I still haven't figured out. It does not happen in Visio 2010.