I spent a lot of time on this issue earlier and finally found out what is going on.
Today I added a store to my application and although everything deployed (using manual xcopy because I have spaces in my path) the new Store was not found by storemanager.
Checking the files again, app.js had been updated but designer had not. Remembering that Aaron had mentioned that designer.js is legacy I deleted it and had also delete designer.html and switch to debugging through app.html.
I suspect that this will be an issue for people who have used earlier builds of Designer and switched over to Architect.