Backup Problems When Automatically Sync Is NOT Selected

Because I have a huge iTunes library of over 150GB, I always Manually Sync my iPod's and iPhone 3G.
Now with regard to my iPhone 3G, I have noticed that recently when I have downloaded some Applications from the Apps Store via Wi-Fi on my iPhone 3G, after my last Sync with iTunes, when I connect my iPhone 3G to iTunes again, iTunes says it is performing ‘a backup'.
But instead of transferring these new Apps/files over to iTunes it fails to copy them over. ~ Until I updated my iPhone 3G’s software from v 2.0, to 2.0.1, iTunes would always ask me if I wished to transfer purchases from my iPhone 3G to my iTunes account.
Anyhow, I decided to try the +"File|Transfer Purchases From XXXXX iPhone"+ Menu command, but this does not work. Instead, iTunes states in its top window that it is transferring the Applications that have been installed via Wi-Fi.
But that takes about three seconds, and nothing is in fact transferred. I have checked in both places where they should be if successfully transferred over, and that is the Applications window in iTunes or in the folder +"Mobile Applications"+ within the iTunes folder itself.
Both are missing the files that are supposed to have been transferred.
I have read somewhere that if you do not use Automatic Sync with your iPhone 3G, then backups are not always carried out correctly.
Can anyone advise me on this as well as my above problem?
II did find one reference in Apples online support called: "iPhone and iPod touch: About backups" [You can find this at the following Link:] http://support.apple.com/kb/HT1766
Unfortunately, this only covers the process of backups if you synchronise automatically.
So, has anyone and ideas or suggestions pleas?
All advice gratefully received.

I am seeing the same issue between my laptop and desktop. They are both in the same time region, both timestamps are up to date, and both are running the current revision of Firefox. Does anyone know if the add on DNT (Do Not Track) or Privacy fix will block sharing tabs across PC's? Thank you in advance.

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