Safari freeze only fixed by tab change

I've been searching for a reason for a Safari freeze issue with an app I developed, but so far haven't been able to diagnose it.

Essentially the app is a set of HTML pages which uses localStorage and the HTML5 Application Cache to allow it work in offline mode. It's a data entry app used in locations where mobiles are required to be used in airplane mode, then upon finishing (and restoring coverage) a sync process sends all the localStorage data back to our server.

The app has worked perfectly fine for 5 - 6 years on all iOS devices, but after either iOS 9.3, or iOS9.3.1, it has developed an issue where it completely freezes after certain actions. The only way to un-freeze it is to go to a different tab/window, then back again, then it works perfectly fine.

The certain actions involve jQuery element manipulation - essentially there's a bunch of rows of fields for data entry, and when you've finished a row you can save it to localStorage. I animate the removal of the row and insertion of a new clone, to make it obvious what's happened. It's after these actions that the whole page becomes completely unresponsive to finger taps.

It doesn't happen in Chrome at all. Only Safari.

Additional info: The version of jQuery running this is very old (1.3.2). Updating it is not out of the question, but it would require a lot of work to replace deprecated functionality so I'd like to avoid it. I guess the fact that it's worked fine for so long makes me wonder why or what in the iOS upgrade would make it stop working. Plus the method of overcoming it (switching tabs, then switching back) seems at odds with the jQuery library being the problem.

Thanks,

beej.