OK, I have been having the same problems as everyone else in this thread. I have Windows 7 Ultimate, 64-bit, and since the iTunes update synching was having multiple errors. After a lot of experimentation I have fixed my synch issues by doing the following:
1. The inability to back-up when connecting the iPhone 4S to itunes via USB cable:
-This was fixed by resetting the lockdown folder. Steps found at http://support.apple.com/kb/ts2529
-Be aware that after resetting the lockdown folder, you will need to input your passcode into your phone (if you lock your phone with a passcode) the first time you reconnect your phone via cable
-After the lockdown folder is reset, connecting via the cable allows backups to function again. The error does not return after restarting iphone, itunes, or computer, so I think that permanently fixes the error
2. The inability to sync apps when connecting the iPhone 4S to itunes via USB cable:
-This is the bigger issue IMO. I had noticed that apps were not synching between my computer and iphone even when synching over Wi-Fi, even though no error messages were displayed.
-After MUCH experimentation, the only way I got this to work was to disconnect the iphone from my computer, sign out of my Apple store account on BOTH my iPhone and itunes (on my computer), restarting BOTH the iPhone and iTunes, signing BACK onto both, and then reconnecting the iPhone to iTunes. Note that the first time I reconnected them after signing back in, the error still persisted. However, unplugging them and then plugging them back in synched apps for the first time since the problem came up, so I have hope.
I am confident that the backup issue is fixed by following the steps noted in #1 above. I'm not as confident about #2 fixing the app synching issue, but it's working for now.
I hope this helps, at least until Apple fixes whatever they did to this app.
FYI I'm running iOS 5.1.1, the last iteration before iOS 6.0.