How do I get ios5 devices to sync their directly downloaded apps with iTunes ?

I have an iMac /Lion, iPhone and iPad, previously on MobileMe and an iPod touch, never connected to mobile me. I have transferred MobileMe to iCloud.
I have found that programs, downloaded directly to my iPad, will download to my iPhone(directly), but not the iPod.
When connecting directly to my iMac, to sync, I get the message : -
Some of the purchased items on the iPhone/iPad “…[name]..” could not be transferred to your library, because you are not authorised for them on this computer. Interestingly it shows the icons on the iPhone display on the iTunes display.
Transferring the other way is okay.
I suspect that this is due to confusion of the two passwords (MobileMe and apple id).
I’m afraid to re authorise the computer as I don’t wish to lose other programs.

P.S.  I've tried - File/Transfer Purchases

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