Delete app from iPod Touch, but still shows up in iTunes

I've deleted a couple of apps from my iPod Touch, but after a sync they are still showing up in the iTunes apps tab with my iPod plugged in. They are both unchecked, so that they will not sync, but I can't seem to delete the app itself from my computer. In the previous version of iTunes, you could manually delete an app from iTunes and it would be gone, not just unchecked.
Any advice?
Using latest version 9.

Try going into your iTunes/Mobile Application folder (wherever that is on Win XP) and deleting the .IPA for that particular app. Thats how I permanently delete my unwanted apps as simply deleting them in itunes or on the touch desnt get rid of them completely and iTunes always trys to put them back in there as it stayed stored in my application folder.

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