Can't make ipad sync apps to new computer's iTunes

I have a slightly strange problem. In Sept 2012, I got a MacBook to replace a Windows laptop. I transferred all my itunes music across and used 'transfer purchases' from my Ipod Touch to transfer all the apps to the itunes on the mac so I could keep all my apps. I then ticked the 'sync apps' box, and synced and everything works wonderfully, all my apps are still there etc and I can download them from the app store etc on the ipod.

However, when I did this with my iPad 2, it never changed from syncing with the old laptop. Under iTunes wifi sync on the ipad, music,movies,podcasts, books and tones are synced with the new macbook, and for some reason apps, itunes U and movies are synced with my old laptop. I can't download any new apps or music on the ipad from the itunes app/appstore app either (the buttons just don't do anything). Nor can I seem to, no matter how hard I try, make the ipad sync apps with the new macbook. The apps themselves work just as they ever used to.

I understand with itunes 11 the 'sync apps' button has gone, so I tried transferring purchases and then syncing, to no avail. All my apps show up in the corect position under the 'apps' tab, but they just won't sync.

I have some access to the old laptop, but it is 200 miles away and I can't access it for several weeks at least. There's nothing in the apps themselves that is absolutely vital for me to keep (although obviously it'd be annoying to lose all the data stored in them, such as game saves).

Can anyone help?

Thanks,

Pippa

Edit: Strangely, I can now get it to delete apps, by deleting them from the apps tab on iTunes, it goes all the way through the sync, but finds an app to sync (generally just one), gets halfway through that then cancels the sync. However, it has deleted the app I selected for deletion from the ipad. I still can't downalod anything from the itunes app.