HT1977 My Computer crashed so I have had to download iTunes all over again. The problem is now I can't sync my Apps to my iTunes. It doesn't let me arrange them or anything when plugging my iPad in. The screen is greylike and won't let me select anything

Hi Guys,
My computer crashed and I lost everything. I got a new one and downloaded itunes all over again. When I plug my ipad in even after authorising my computer it will still not let me edit anything on the ipad. The screen is grey like on the ipad section and i cant select an app or anything. I have transfered purchase apps but all it does is take movies and tv shows accross. It wont transfer the apps into itunes. Please help

As far as I know, iTunes will still not change anything until you click on Apply in the lower right corner. I fiddle with my settings all the time - just so I can get a sense if what to expect should I make any changes - and I have never seen anything happen to my configuration unless I click on Apply in the lower right corner of iTunes. Not only that - you have turned off auto sync so as far as I know you still have to click on sync or apply in order for the iPad to sync with iTunes.
That doesn't mean it will not happen, I've never seen it happen - is all that I'm saying. I'm sorry but I'm not sure what will happen, but the only reason that I can of why the apps will not transfer is because of the manual manage setting. I could be wrong about that as well.
Look at this discussion - which I have referred quite a few users to read. I know this process has worked for a number of people that have read it and used the instructions in it. Maybe we are missing something - what that would be - I'm not quite sure, but take a look.
https://discussions.apple.com/thread/3305461

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