iOS 'Web App' has different localStorage than Mobile Safari

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I have a webapp for iPad with the meta tag:

<meta name="apple-mobile-web-app-capable" content="yes">

When I open up the app from the homepage (web-app-capable version) or type in the address in Mobile Safari the contents of localStorage are different. I have confirmed that the addresses are identical by printing location.href.

All changes made to localStorage while using Mobile safari are reflected in the web-app-capable version, but changes made in the web-app-capable version are not reflected in the Mobile Safari version.

The domains are identical, localStorage should be identical. What in the world is going on? Can this be fixed?


Update - Solution: Following suggestion #2 from the accepted answer (forcing the user to be in fullscreen mode) I added this bit of code:

if(("standalone" in window.navigator) && !window.navigator.standalone)
    window.location = "instructions.html";

So, if you are using a browser that supports standalone mode, and you are not in standalone mode, redirect to a page (instructions.html) which shows the user how to add the app to the home screen.

Thank you to everyone for their input!

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