Apps purchased on iPad are being deleted when syncing with iTunes

Hi,
I am having a problem with the apps that I purchase using my iPad not syncing with iTunes. I have purchased several apps and books. When I use my iPad to make the purchase and then plug the device into my computer to allow it to sync, iTunes goes through the process of backing up the iPad and then transfering purchases over. When it gets to the step for syncing tracks it goes and removes all of the apps that it just said it was transfering the purchases over for. Nothing I do seems to work to fix this issue so that the apps aren't removed when I sync. So far the only ones that stay on my computer and device are the apps that I used my computer to buy and then are synced onto my iPad. Please let me know what to do about this as I have lost several apps.
Thanks
Josef

I am not sure what the problem could be.
You may want to try disabling auto-sync, make some purchases on your iPad, and then transfering the purchases and see if they show up in your iTunes library and the checkbox for the apps are checked for syncing to your iPad. If they are then you can try syncing and see if that deletes them from your iTunes library.
The link for instructions on transfering your purchase is as follows:
http://support.apple.com/kb/HT1848

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