Did you try selecting the apps to sync in the Apps Tab of iTunes rather than drag and drop?
This explains how to select apps to sync.
Connect the iPad to the computer and launch iTunes.
Click on the iPad name on the left side under devices.
Click on the Apps Tab on the right.
Select all of the apps that you want to sync.
Click on the Sync Apps Heading.
Click on Apply in the lower right corner of iTunes
If running iTunes 11 - go to View>Show Sidebar at the top of the screen to enable the sidebar.