Latest iTunes update will break your iPhone!!

The situation:

Yesterday I updated iTunes on my MacBook Pro... this morning it was still open and I had to force quite iTunes to restart it.

Additionally, I woke up this morning and morning and the Passcode on my iPhone was not working. It is the same passcode I've always had and I have not changed it. NOTE: I did not connect my phone to iTunes at anytime, so not sure that was the cause of my isssue.

I did everything I could to try and rectify the Passcode issue and the only solution seemed to be that I had to restore my iPhone from a backup. My backup was a few days old, which was fine by me to use.

After the long process of resetting the phone to factory settings and restoring the from the iCloud backup, it then began to delete every App from the phone that was not an Apple App.

I got on the phone with Apple Support and the person I spoke with couldn't tell me why this was happening, so put me onto a 'senior advisor'... he told me that the backup might still be loading and I should wait until all my Apps finish updating... when it finally seemed to finish, everything was gone off my phone except the Apple Apps.

He then proceeded to give me instruction on how to re-install Apps from the App Store... um, duh.. I know how to install a freaking App... I want to know WHY were they deleted and WHY won't the backup work??

He finally admits that there is a bug in the latest version of iTunes and the same thing happened to him and there was no way around it.

Are you SERIOUS??? You just tried to tell me 2 different things in the same conversation.

What I now need to know is:

1) when will the bug be fixed

2) is there anyway to stop iTunes from deleting all my Apps and their data?????

I am not concerned about games or other time wasting apps, I'm very concerned about the app data as I use a number of Apps for my work and have lost a lot of important information.

Is there a way to retrieve this data or stop the apps from "updating" after a restore?????