Vojo:
I’ve been living that life for years using 2013 Professional at work and 2003 at home. I have a common stencil (my Kencil) that I use everywhere all the time. Never saw the behavior you describe. Yes, it complains if I try to update it while it’s open in another instance, but when I close the other instance, update the stencil, then re-open the instance, everything is sweetness and light.
Sounds like you may have a cache-type of problem? If you were in a browser, I’d recommend clearing your cache or hitting ctrl-F5. No idea how to clear Visio’s cache, whatever that may mean.
Good luck,
- Ken