Problem with sync in iTunes. Installed applications do not copy

Hi,
I run Win XP. I have an Iphone 3G running 2.2.
I have 100+ apps installed on the phone. When I sync, it always downloads from the iTunes Store the last 20-30 apps that I have installed on the phone. It takes 10-15 minutes everytime I sync. (it used to take 30sec -> 1min before).
These last apps do not appear in:
Devices / Name /
I have checked on the folder C://My music > iTunes > iTunes apps. These 20-30 apps are not copied there with the other apps.
I have uninstalled iTunes & reinstalled it. Same problem.

Thanks for your response.
Yes I had the tick box checked, as I had previously synced the playlists to the phone. (I'm correct thinking you're referring to the check box under the MUSIC => iTunes Library => Playlists heading?).
When I have my phone connected the playlists which I have synced become ticked/highlighted, it just appears that they don't update any changes that have been made since they were first transferred.

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Problem with sync in iTunes. Installed applications do not copy

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