Apps keep disappearing from itunes

Ok, i am not quite sure what section to put this under as it pertains to a couple different areas i think..
Anyway, i upgraded my itunes and iphone software this morning as i was getting the common and annoying error message -50 and after looking around and trying various proposed fixes non of them worked so i decided to upgrade to the latest versions.. Well that didn't help..
But now what i have found is that whenever i connect my phone to my laptop and open itunes, itunes keeps uninstalling all but one of my apps!! I then have to navigate to where the downloaded apps are on my harddrive, drag them in to the app section in itunes, go in to the iphone on itunes and resync again! In the process i have lost all my photos on my phone because they were all transferred across in to the photo-sort app, obviously all the game data is now lost too (not a biggie)..
My phone is not jailbroken or anything. All apps were purchased legitimately. I am now starting to get extremely frustrated with this so any advice on what is the problem would be greatly appreciated!

Have you tried restarting or resetting your iPad?
Restart: Press On/Off button until the Slide to Power Off slider appears, select Slide to Power Off and, after It shuts down, press the On/Off button until the Apple logo appears.
Reset: Press the Home and On/Off buttons at the same time and hold them until the Apple logo appears (about 10 seconds).
If these don't solve the problem try:
Settings > General > Reset > Reset Home Screen Layout

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