Issues syncing apps between itunes and ios devices - changed itunes store

I have had an iTunes store account for several years with the same apple ID.  Initially I connected that apple ID to the Belgian store and about 2 years ago I changed to the UK store, but still with the same apple ID. 
Since I have several IOS devices, I prefer to use iTunes to update any apps I have downloaded and then sync them onto all my IOS devices using my local network rather than downloading accross the internet each time.  When I view the apps in my library it says a number of updates are available (right now there are 9).  but when I click on the button to go to the store and retrieve the updates - itunes store says "No Updates are currently avaialable" and suggests I sign in with a different ID.  However, I don't have a different ID. 
This seems to be that any of the apps I puurchased in the Belgian store prior to switch to the UK will not update.   For a while, as a resolution, I was able to download updates on one or more of my IOS devices sucesfully whicever store I purchased them from and then when I synced back to iTunes, it updated them in the library.  Wasn't very pretty but it worked. 
Now after upgrading to iTunes 11, although I can still update the apps on my IOS devices, when I sync it no longer transfers the updates to the iTunes library - I haven't had iTunes 11 long enough to determine if it's related to the same store switch issue or if it's a general problem.
Anybody got any similar experiences or solutions to consolidate all my purchased apps (which ever store) into one, so updating is transparenet again?

(A) Reset iPad
Hold down the Sleep/Wake button and the Home button at the same time for at least ten seconds, until the Apple logo appears
Note: Data will not be affected.
(B) Reset all settings
Settings>General>Reset>Reset all settings
Note: Data will not be affected but settings will be reset.

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