ITunes is saving my Apps in two different places

When I buy an App in iTunes it is downloaded to
~/Music/iTunes/Mobile Applications
But when I by an app direct from my iPod and then sync with iTunes, it appears on my hard drive in:
~/Music/iTunes/iTunes Media/Mobile Applications
This means I have two Mobile Application folders, both with unique content.
I have consolidated the library and have updated to the new media organisation.
Is this normal behaviour for iTunes and iPod to use different Mobile Application folders?
Why isn't iTunes defaulting to the new media organisation and putting Mobile Apps inside the Media folder?
Thanks for any help.

Further Investigation:
1. I thought that maybe ~/Music/iTunes/Mobile Applications was a legacy folder, so I deleted it and downloaded a free App from the app store (using iTunes)
iTunes created the folder again and put the App inside it!
2. Another strange discovery - If you consolidate the Library to an external Hard Drive, iTunes merges the contents of the two local Apps Folders and puts them in ExternalHD/iTunes/iTunes Media/Mobile Applications
I wonder why it is keeping this legacy folder in the Home Directory, and why it is still putting new Apps there, but then putting new Apps from the iPod/iPhone into iTunes Media

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ITunes is saving my Apps in two different places

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