8chan features script
Indeed. It's because the script overwrites the display rule for #navTopBoardsSpan and will only set it to "none" if you leave the "Hide Default Boards" textarea empty (instead of setting it as "all" to allegedly remove the default boards, as instructed.)
The CCS "To hide the default boards at the top: #navTopBoardsSpan {display: none;}" does not work when this script is active.