All my apps won't sync to my ipad.

I received a new ipad because my original wouldn't charge and now all my apps won't sync, only a few will.  How do I get all of them to sync?

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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