By default, Carbonite toggles between maximized and minimized at the press of the minimap hotkey button (default: M). These two maps can be adjusted independently, and is saved on a per-character basis.
It sounds to me like your maximized Carbonite map has been resized (intentionally or unintentionally) to be close to the same size as your minimized Carbonite map. Try pulling one of them out to the middle of the screen and resizing it, then toggle between them with M until you find a setup for both maps that you feel comfortable with.
Alternatively, if you have one character that you're happy with both maps on, you can open the Warehouse (chest button on the Carb map), right click that character's name, and select Import settings. You can also access this feature from the Carbonite options menu (which includes importing settings from other realms too). This will import all character-specific settings, including map size and positioning.