Itunes sync deletes downloaded apps

Getting very frustrated with my new iPad and iOS 5.1. I've tried searching and can't find any assistance. Here's my situation, brand new iPad running iOS 5.1, exising iTunes (updated to the version of the week). I am not set up to use iCloud for anything. Whenever I sync with my desktop iTunes will delete, without any warning, remove any apps that were downloaded directly (over WiFi) to my iPad, removing the app and any data it may have saved.
1. I have reset warnings on my iPad several times, I still don't get any.
2. I have tried "transfer purchases", iTunes never "sees" any purchases and doesn't download them.
3. I have tried a complete wipe and reset as a new iPad.
4. I have tried a complete wipe and restore from a backup.
5. My iPad has not been synced with another computer.
6. I have reset my iPad, rebooted my computer, even changed cables.
7. I only have one Apple ID.
8. I have skipped setting up my Apple ID directly on the iPad, as well as setting it up there first.
If iTunes installs the app itself, then it leaves it alone just fine. It is just apps that it has not installed.
This behavior does not occur with any of my other devices (iPads or iPhones). Just the new one, it is also the only one running 5.1.
Basically, any apps I buy and download on the device, I have to go home, into iTunes, have it check for new purchases, download them. Sync (and watch them get wiped out), then check them in iTunes and sync them back.
Very frustrating to say the least.
I tried calling Apple support. They suggested #4 and #3. Tried both. Neither worked.
I can reproduce this behavior every time.
Has anyone seen this before and know of a way to "fix" it? I have no interest in going to iCloud with my data, I prefer my iOS devices with encrypted backups locally.
Thanks.

>>Basically, any apps I buy and download on the device, I have to go home, into iTunes, have it check for new >>purchases, download them. Sync (and watch them get wiped out), then check them in iTunes and sync >>them back.
Hi Scott,
I have the same problem as yours on my iPad1, and also, just like you, I do not have that problem on my iPhone4, also my wife does not see that behavior on her iPad2.
That said, and although I do not have a true fix, I can show you how I have it setup to make it a little less disrupting as what you are doing now...
on iTunes, in Edit, Preferences, Store, I have an "Automatic Downloads" checkmark for all 3, Music, Apps & Books so that anything that I buy on my devices are automatically downloaded to my computer.
So when I purchase (via wifi) an app directly on my iPad, or when I download (via wifi) directly on my iPad an app that is on my computer I do the following:
I open iTunes on my PC (the new app that I purchased via wifi is already there).
I plug my iPad to my PC.
iPad shows automatically on iTunes.
I select the "Apps" tab on top of screen (the one after "Summary and "Info").
I have a checkmark under "Synch Apps".
I do not have a checkmark under "Automatically sync new apps" at bottom of apps list column.
I type the name in the search field of the app that I downloaded via wifi to my iPad (or just look manually for it thru the apps list column).
I checkmark it (because it is not checkmarked and it would remove it from our iPad).
Now if I synch, the app is not removed.
Hope I was clear enough...and pls let me know if you find a permanent fix...
J-C

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