The 'shaded' areas seem to be happening since Ant updated the plugins so there seems to have just been a change in how the map renders. So eventually the whole map should be more like that I think.
I have always assumed that the blocks on the map represent the chunks in the world, which could be 16x16
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everyone else: I came to find out about the grey shaded bits and you have no clue :(
maybe they are bits that have been explored but not visited recently?
That yellow 8px square in the center is the size of a 1x1 block... but it's actually representing a torch (which is much thinner than a block).
I guess you can say, every coloured square on the map is a single block, but it's colour may be different to it's actual colour based on having something on-top of it which is actually smaller than one block (torches, signs, doors, ladders, flowers, etc).
Oh, and also in-game the blocks are not solid colours, or sometimes not even close to those colours.
Still it looks like the new darker map images are improving things - if you head north from the Citadel until you reach another shaded area - the dark green in there is grass, which used to be coloured purple as you'll see if you look at the surrounding areas.
Chrome (here at least) gives different results to IE and Firefox (when zoomed in), the blocks are blurred instead of square so some scaling/blending thing going on.
