I know this question was asked a while back but thought I would post my solution anyway in case anyone else needs it.
To get a separate colour for the bottom section of your box plot you need to create two separate box plots. In the first one set the Box Plot Bottom to be the same as the middle value (i.e. Fractile (Value, 0.5)) then in the second box plot set the bottom one as usual (0.25) and set the top one to be 0.5. You will then get two different coloured sections.