IPad syncing apps to old library, everything else to new library

This has me puzzled and I've not been able to find a definitive answer.
I used to sync my iPad to my MacBook Air, but recently transfered my library over to a Mac Mini (authorised, same Apple ID etc). This appeared to be working fine, but I've just noticed that my iPad appears to have split where it syncs now, syncing apps from my Air and books, movies, music, photos and tones from my Mini.
I've popped a link to a screenshot below to explain what I mean (Lilburne is my Air, Dickon is my Mini)
In iTunes on the Mini I can't see any way to force apps to sync from there - there's no 'sync apps' checkbox in there.
I've got the same situation with my iPhone 5 too. Bizarre! I'd appreciate any help to find the probably foolish thing I've either done or not noticed!
Thank you :)
http://img69.imageshack.us/img69/2594/l4py.jpg

Thanks Griff
I've checked out those steps and it doesn't really answer the issue - this isn't a problem with WiFi syncing (although that is really flakey I've found!), more a problem that part of my content on my phone is syncing from my new computer, but apps are still listed as syncing from my old computer on my iOS devices.
It's not a dramatic problem as obviously I can manage app updates / deletions / installations on the iOS devices directly anyway, but it's an odd one.
I do still have the Macbook Air I used to sync my devices to, but have removed the iTunes content from it.

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