I had diffculty getting this to work also and instead changed the default map background to a light green in all rom_col sets:

map_colours
default map areas R24, G29, B24

This makes the white stand out a little better and is more in keeping with English green fields ! Works in both split and wide screen.

I'm not 100% sure but I think rom_col is wide screen, rom_col1 is split screen, set each set being a pair (so brown set is rom_col2 and rom_col3, mini set 10 and 11) Are you sure you've changed both sets? Try opening two navtweak windows - one pointing at original navboot, other at customised. Go through each pallete checking for differences.