Apps will not delete - they keep coming back!

I have the latest iTunes (10.1.0.56) on Windows Vista Ultimate 32 bit. This occurs on my iPhone 4 with iOS 4.0.1, as well as on my iPad 3G with iOS 4.2. No, not jail broken either.
I have iTunes managing the apps. I have over 1200 apps, but obviously need to get rid of most of them ...and most are free or were free. I don't want to delete them from itunes, as it helps me know what I've purchased in case I need to reinstall something.
Anyway, i delete apps from my iPhone and iPad, and when I sync, they keep getting reinstalled. It even recopies apps the I have not deleted. While doing this, the iPad will often reboot while syncing, and it just boots up again, and continues. Also, apps that I have installed directly on the iPad or iPhone, get deleted when syncing. I suspect it's tha iTunes is trying the keep the list in sync, but the list is messed up in iTunes. And, I can't manage it in iTunes because of the volume of 1200 apps makes scrolling in iTunes incredibly slow, and often just crashes iTunes ... Which just means it can't manage the list there.
I have already deinstalled itunes, and reinstalled it. I've also already restored my iPad to new, and still the same issues.
Is there a downside to self managing my apps? For instance, is the data still backed up? And purchases too?
This is incredibly frustrating. Seems like others are having similar issues:
http://appletoolbox.com/2010/09/itunes-10-iphone-ipod-or-ipad-wont-sync/
Thx.
My contacts and calendar syncs fine.

Here's an update, still the same issues:
1. I Restored again, and this time turned OFF the App syncing, so that I would do it manually. But that's a pain because the only way to get apps on the device is to find, then download each one manually again from the AppStore. If I only had 10 apps, that would be fine, but I don't. Also, I'm not even guaranteed that my settings for these apps would be backedup.
2. So, I then dragged an App from the App library into iTunes, to the device, and this just automatically turned on App sync. So I guess that's the only option, to turn on App sync.
Issue A: Now, I still have the issue where if I download an app to the device directly from the App Store, and then sync, itunes will still delete it from the device. Only where I have downloaded it into itunes, then dragged it back to the device, will it stay there.
Issue B: When I resync, itunes still wants to reinstall all the existing apps (it says "Installing ...", even though I haven't touched them, nor have they been updated recently).
This is very irksome!! Anyone have a solution? Please. Thx.
- Mac

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Apps will not delete - they keep coming back!

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