I'm having the same issue - FT on iPhone 4 no longer working.
Wiping the phone brings FT back to work, but as soon as I re-apply my backup via itunes or icloud it stopps working.
I've scheduled an appointment at an Apple Store's Genius bar today. Guess what they said?
"You have to start from scratch. There is no other way to get this working again. I do understand you, but it can happen that a backup can become corrupt, especially when you have carried your configuration over multiple ios upgrades. All you are going to lose is your imessages and WhatsApp messages."
Really Apple? Really? This is not a solution!
What about wifi network keys, certificates, passbook app data, bookkeeping apps, other chat application data, account and history data of various 3rd party apps to just give you a few examples....
Imagine a company has lost an important file structure and is unable to restore from backup and the IT guy tells you "well, I think you have to start from scratch". Sorry, not acceptable!
Hopefully some big media will catch up on the issue soon, so finally this post gets the attention it deserves.
Apple, please do something!