Deleted videos still in iTunes

I set all my devices to manually manage so copy mp4 video files to my iPad and delete locally after I watch them. However, the deleted files still show in iTunes when I reconnect. The space usage seems to adjust appropriately on the iPad but I'm concerned the space isn't really freeing up and it could cause problems if I download something new. It's also a bit of a pain to have to delete every files twice. Is anyone else seeing this? Is there some setting I'm missing?

Thanks!!