It's a shared texture with the boxes sharing the same area in the uv-map.
Have you played the escape from terra map? It opens with everyone's colonizer in the same gravity well trying to escape from an overrun earth. I haven't looked at the code for the map, but it might be worth looking at.
I'm not much of a model texturer but I do graphics for a living (oh, the irony).
When the graphics programs convert/save/compress file types, they all have artifacts and formats. It may be the color squares you see aren't saving uniformly--meaning they have distortion--or are a graphic type that renders as un-uniform/distorted when seen in alpha. Basically, you are then seeing the inconsistencies in one prgram view that another might not have.
The other thing from the "on-off" boxes may be that the alpha layer isn't being applied to the entire portion of the image you want specified. I haven't looked yet but if you have to tell it where to look on the sheet, the alpha layer may not be in the right place or is a shape that doesn't cover where you think it does.
Is it Gimp or something else? I bet Thoumsin may be able to explain it.
On a side note, I read your post about the Terra map and gave it a peek and I have a little more elaborate map pretty similar to it I did way back (It was my alternative to modding--using unique maps).
It's a 1v8 map--"Vasari vs. All Others". it has a lot of tricks and twists in it and I'll tune it up and post it today sometime. I think it's fun and the Vasari has to raid commerce (and not lose his ships in the process) in order to gain some start income.