If I understand the issue you had, I had the opposite problem because I didn't know what the Store pins did. But then I tried it and it has improved my productivity enormously.
My newest store is the one in my Signature - late in the alphabet, and I have so many stores it does not normally appear on the dropdown menu under My Stores. Previously, I was hovering over my Creator Icon, then clicking on My Stores, then scrolling down to the bottom of that page to enter my Worldesigns Store. Annoying!
Then I realised there was a pin next to it, so I clicked it - and got the result that freaked you out with yours. The only store that showed up was the one I wanted. AND it's now right at the top of My Stores when I hover over my Creator Icon.
So Store-pinning has it's uses; and is especially useful for me, with so many stores. But it's probably not for everybody.
