ITunes 9 removing all my apps at syncing

hello, I got iTunes 9 last night and had no problems at all, I loved it, but when i wanted to sync my ipod touch 2nd gen. 16 gb, even though the app tabs has checked all the apps i want (almost 90 i think), and i got the 3.1 update, iTunes will start removing allll my apps, i have to stop the syncing otherwise i lose them all. When i apply the changes after rearragment sometimes it will show up an alert saying that iTunes will remove 73 apps from my ipod, are you sure to continue?
i haven't seen this problem anywhere, have you? any ideas?

Different iPod but same principle, maybe...
When I first synced after installing iTunes 9, I got the same error message that it would remove my 19 Games (Apps to a Classic)
This was due to a bug in which I had to reauthorize my PC, even thought it was already authorized. After I did this it worked fine.
Now I need to email Apple as I have lost an extra Authorization. Definitely a problem at their end though
Hope this helps

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