Your Transparent color isn't.. transparent.

As you probably know, the very last block on the "blue" layer should be completely blank - that is set as default for the entire map. When you view the "green" layer the map still shows the blue layer, just as somewhat transparent. (It's reversed when you view the blue layer)

Basically, the non-transparant "pink" block is still showing on the lower layer, so it looks fogged.

Not sure how to set transparent color in PaintShop, so I can't help you beyond that. I think RM2k3 uses an absolute location on the chipset as its transparent color - I'll try to find that info when business school is over..