Transfer purchases only transfers one app at a time

I'm trying to back up my iPad in preparation for installing the new iOS, I'm transferring purchases first, but iTunes only transfers one app each time I click transfer purchases! This never used to happen, any idea how to stop it doing this, how do I transfer all the apps at once?
Also, when I sync my iPad or iPhone, iTunes frequently moves the apps around on the screen of the iPhone/iPad, taking them out of folders etc, and re-installs ones I've deleted from the iPhone/iPad. How do I get it to stop doing this? I just want it to back up whatever is on the iPhone/iPad, not change it in any way.

My iPhone4 and iPad2 are both doing this same thing (only transferring one app at a time). It is really frustrating because I purchase a lot of apps from my phone or ipad and it takes forever to keep clicking 'transfer purchases' over and over again for each individual app every time that I sync or update. It would be great if someone could figure out how I could enable it so that all of the apps transfer to the computer at once.
Regarding the second part of your post, I've had that same problem before. When doing a sync, after backing up my iPhone/iPad, the apps are updated, and when the screen comes back all or most of the folders are missing and I have more apps than can fit in the display. Or sometimes it happens after upgrading the software or restoring it. After reading other posts about the same thing, I've found that doing a restore from your latest backup will usually restore all of your folders, too. The trick is that you might have to do the restore twice. Try to restore your phone from a backup and when it comes back, if the folders are still missing, do the restore one more time. I don't know why doing it the second time works, but it has worked for me on 3 separate occasions when nothing else would. I know that it is a pain to have to waste the time of doing an entire restore (especially if you have to do it twice), but it is less work than having to remember and recreate your folders from scratch.
Message was edited by: bigdaddylongluv
Message was edited by: bigdaddylongluv

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