This is a sync operation, not a copy. That means iTunes tries to keep the folders/albums on your iPad the same as what you have selected for syncing in iTunes. By choosing a new folder you are not telling iTunes, add this folder also. You are saying, I want this folder instead of the other one.
To sync more than one folder of pictures, put both folders that you want to sync into another folder, and choose that folder to sync. Once you do so you will have the option to sync all sub-folders in the main folder, or just selected folders. To add another album/folder, just create a new folder int he main folder and add pictures to it. iTunes will make the change automatically on the next sync.
I recommend creating a main folder and one level of subfolders (more will not sync), then placing copies of the pictures you want to sync in the respective folders. Each subfolder will become an album in Photos on the iPad.
iOS and iPod: Syncing photos using iTunes
Another thing to keep in mind is the only way to remove albums synced through iTunes is to remove them from the folders on the computer, or change the sync settings in iTunes, and sync again. You can not delete this kind of album or the pictures in it directly on the iPad.