I had the same problem. Authentication broke or disabled JS on the page that triggered the cache manifest when we launched the application in full screen from the main screen.
As a job, starting with a mobile safari, we save the page on the main screen, which is a duplicate version of the page from which we want our cache manifest to be executed. Then, as soon as you start the page from the main screen, we forward the duplicated page to the real page on which the cache manifest works.
This causes the login, but does not interrupt JS from the cache manifest, as it is technically requested on our "fake page", although the user is immediately redirected to the correct page, where their cache download then starts successfully.
This seems like a bug in the full screen mode of mobile Safari. Hopefully these things will be fixed in a future release. Hope this helps.
UPDATE: the above fix did not finish working for us, since the fake intro page is not included in the manifest, so it does not load after offline work. bummer. we ended up just launching caching from a mobile safari, so any updates made should be done through the browser, and not in full screen mode.
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