Found a temporary solution that fixes everything, including leaving JavaScript on and clicking links in mail.
This is for jail broken users only and thanks to @paulpols
Using ifile, edit com.apple.swcd.plist and then change the value of com.apple.SharedWebCredentials to false.
According to Paul, this means we will have to manually sign into sites, but that's a quick solution until there's a proper fix.
I'm now digging through files to test things.
1- if possible to clear it out / delete it and let the iPhone repopulate it
2- see if there's anything weird that specifically needs to be deleted.
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The ones similar to me are, iTunes U, Google cast, Airbnb, swarm, IMDb, Uber