There is an option in iTunes settings to sync apps between your computer and the iPad. Make sure it's not selected. I suspect you have it checked and then, since the apps don't exist on your PC, it wants to remove them from your iPad.
Just a thought.
When you purchase an app through the iTunes Store on your iPad then you sync it with iTunes on your computer, it transfers the app to your computer. It does not delete it from your iPad! The same holds true for any other content like music, books, podcasts, movies, etc.