I have a similar problem (I think - or at least it may have the same root cause).
I have created a custom stencil from the supplied stencil "BPMN Basic Stencil". Did this using "Save As" of the BPMN Basic Stencil. So far so good.
I close everything, create an empty document, check to make sure there's no "Document Stencil" elements (again so far so good) but...
When I drag in my pool/lane from my custom stencil, Visio annoyingly opens the "BPMN Basic Shapes" stencil thus making it the active stencil in the left hand pane.
My users (and me if I'm not paying attention) then start using the supplied stencil shapes rather than my custom shapes.
EVERY other shape is fine (ie. they do not open the supplied stencil). Any idea how I can switch off this behaviour?