If you have a file in the same folder as the game with the name icon.png or the same name as the game (except with .png at the end), Dolphin will use that as a banner instead of the regular one. If you have files there that you don't want to be used as banners, you can rename them or move them. If you have some reason to keep the files there with those specific names, please tell me. I don't think there are many people who use this functionality for things other than DOL and ELF files, so there might be a reason to change it.
The reason that they became smaller is because an update to Dolphin made the scaling preserve the aspect ratio.
The reason that they became smaller is because an update to Dolphin made the scaling preserve the aspect ratio.