What do the colours and dots on the map mean?
Two different things are being shown, and they are kept apart on purpose.
Dots say what a Board of Education is doing. A green dot means a Board in that prefecture has an opening now. An orange dot means one closed within the last 60 days.
The wood of a piece is about you. A prefecture you have marked as somewhere you would work is stained a different wood from the rest of the board, and a prefecture set as your home base is stained differently again. Nothing you mark ever changes a dot.
A piece in plain wood with no dot means no Board there is yet known to hire ALTs directly.