You have the camera roll photos and the photos that you synced in another folder in the Photos App.
You MUST place all of the folders tha you want to sync to the iPad into one folder. You CANNOT sync two different folders to the iPad other than to place two subfolders into the one main folder from which you sync. If you try to sync a totally different folder from the first folder, the first photo folder will be erased from the iPad.
Place all of the folders that you want to sync into your main photos folder. You can have one level of sub folders in the main photos folder and you CAN select them all to sync.
After you placed all of the photos into that one main folder - select that folder in the Sync Photos From heading/menu in the Photos Tab of iTunes when you sync your iPad. And remember that all of your photos must be included in every sync each time that you sync.